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From: kok <kok...@gm...> - 2013-08-02 06:53:14
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Is it possible for cg pipeline to include the results of other /ab-initio /predictor (eg. prodigal)? Is there any development for this function? Or if I would like to use prodigal in place of genemark (if only two predictors allowed), can I convert the results of prodigal into genemark-like gm_out.lst file for cg pipeline's run_predict as a simple modification? - kok - |
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From: Jay <jhu...@gm...> - 2013-08-02 13:43:15
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As far as I know, there is no convenient way of doing this. The run_prediction script would have to be modified to support running it and parsing the results. On 02/08/2013 22:52, kok wrote: > Is it possible for cg pipeline to include the results of other > /ab-initio /predictor (eg. prodigal)? Is there any development for > this function? > Or if I would like to use prodigal in place of genemark (if only two > predictors allowed), can I convert the results of prodigal into > genemark-like gm_out.lst file for cg pipeline's run_predict as a > simple modification? > > - kok - > > > ------------------------------------------------------------------------------ > Get your SQL database under version control now! > Version control is standard for application code, but databases havent > caught up. So what steps can you take to put your SQL databases under > version control? Why should you start doing it? Read more to find out. > http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk > > > _______________________________________________ > Cg-pipeline-users mailing list > Cg-...@li... > https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users |
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From: Lee K. <ls...@gm...> - 2013-08-02 15:52:09
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I'm returning to the US and back to work on Aug 12. It sounds like a worthy addition. I like prodigal but never bothered to put it in as an option. I think it could be something optional like genemark and would be preferred if not using genemark. In this way, CGP would still be able to have a majority for gene calling even if you don't have genemark. On Aug 2, 2013, at 15:43, Jay <jhu...@gm...> wrote: As far as I know, there is no convenient way of doing this. The run_prediction script would have to be modified to support running it and parsing the results. On 02/08/2013 22:52, kok wrote: Is it possible for cg pipeline to include the results of other *ab-initio *predictor (eg. prodigal)? Is there any development for this function? Or if I would like to use prodigal in place of genemark (if only two predictors allowed), can I convert the results of prodigal into genemark-like gm_out.lst file for cg pipeline's run_predict as a simple modification? - kok - ------------------------------------------------------------------------------ Get your SQL database under version control now! Version control is standard for application code, but databases havent caught up. So what steps can you take to put your SQL databases under version control? Why should you start doing it? Read more to find out.http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk _______________________________________________ Cg-pipeline-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users ------------------------------------------------------------------------------ Get your SQL database under version control now! Version control is standard for application code, but databases havent caught up. So what steps can you take to put your SQL databases under version control? Why should you start doing it? Read more to find out. http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk _______________________________________________ Cg-pipeline-users mailing list Cg-...@li... https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users |
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From: Gmail <kok...@gm...> - 2013-08-03 03:33:35
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Thanks Jay and Lee. It will be great if the option is added. I like prodigal for their better start prediction (from what i get for my test genome) and less false prediction for bacterial genome as claimed. Looking forward to the update, thanks! On 02/08/2013, at 23:51, Lee Katz <ls...@gm...> wrote: > I'm returning to the US and back to work on Aug 12. It sounds like a worthy addition. > > I like prodigal but never bothered to put it in as an option. I think it could be something optional like genemark and would be preferred if not using genemark. In this way, CGP would still be able to have a majority for gene calling even if you don't have genemark. > > On Aug 2, 2013, at 15:43, Jay <jhu...@gm...> wrote: > >> As far as I know, there is no convenient way of doing this. The run_prediction script would have to be modified to support running it and parsing the results. >> >> On 02/08/2013 22:52, kok wrote: >>> Is it possible for cg pipeline to include the results of other ab-initio predictor (eg. prodigal)? Is there any development for this function? >>> Or if I would like to use prodigal in place of genemark (if only two predictors allowed), can I convert the results of prodigal into genemark-like gm_out.lst file for cg pipeline's run_predict as a simple modification? >>> >>> - kok - >>> >>> >>> ------------------------------------------------------------------------------ >>> Get your SQL database under version control now! >>> Version control is standard for application code, but databases havent >>> caught up. So what steps can you take to put your SQL databases under >>> version control? Why should you start doing it? Read more to find out. >>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>> >>> >>> _______________________________________________ >>> Cg-pipeline-users mailing list >>> Cg-...@li... >>> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >> >> ------------------------------------------------------------------------------ >> Get your SQL database under version control now! >> Version control is standard for application code, but databases havent >> caught up. So what steps can you take to put your SQL databases under >> version control? Why should you start doing it? Read more to find out. >> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >> _______________________________________________ >> Cg-pipeline-users mailing list >> Cg-...@li... >> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users |
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From: Lee K. <ls...@gm...> - 2013-08-12 02:35:37
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Hi Kok, I added a script run_prediction_prodigal.pl into source control. It outputs a GFF file of CDS predictions. I also made sure it outputs the training file to the temporary directory because it seems like you are interested in the training files. I also modified run_prediction and the CGPipelineUtils module so that it predicts alongside the other predictors. Lastly, I added an option prediction_use_prodigal = 1 under the config file so that you can enable it for run_prediction. With Prodigal, each gene must have 2/3 or 3/4 majority to be called (depending on whether you use genemark too). I'm new to prodigal, so please let me know if it all looks correct. The command seems simple enough but I don't know if there are any idiosyncrasies to be aware of. On Fri, Aug 2, 2013 at 11:32 PM, Gmail <kok...@gm...> wrote: > Thanks Jay and Lee. It will be great if the option is added. I like > prodigal for their better start prediction (from what i get for my test > genome) and less false prediction for bacterial genome as claimed. Looking > forward to the update, thanks! > > On 02/08/2013, at 23:51, Lee Katz <ls...@gm...> wrote: > > I'm returning to the US and back to work on Aug 12. It sounds like a > worthy addition. > > I like prodigal but never bothered to put it in as an option. I think it > could be something optional like genemark and would be preferred if not > using genemark. In this way, CGP would still be able to have a majority for > gene calling even if you don't have genemark. > > On Aug 2, 2013, at 15:43, Jay <jhu...@gm...> wrote: > > As far as I know, there is no convenient way of doing this. The > run_prediction script would have to be modified to support running it and > parsing the results. > > On 02/08/2013 22:52, kok wrote: > > Is it possible for cg pipeline to include the results of other *ab-initio > *predictor (eg. prodigal)? Is there any development for this function? > Or if I would like to use prodigal in place of genemark (if only two > predictors allowed), can I convert the results of prodigal into > genemark-like gm_out.lst file for cg pipeline's run_predict as a simple > modification? > > - kok - > > > ------------------------------------------------------------------------------ > Get your SQL database under version control now! > Version control is standard for application code, but databases havent > caught up. So what steps can you take to put your SQL databases under > version control? Why should you start doing it? Read more to find out.http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk > > > > _______________________________________________ > Cg-pipeline-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users > > > > ------------------------------------------------------------------------------ > Get your SQL database under version control now! > Version control is standard for application code, but databases havent > caught up. So what steps can you take to put your SQL databases under > version control? Why should you start doing it? Read more to find out. > http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk > > _______________________________________________ > Cg-pipeline-users mailing list > Cg-...@li... > https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users > > -- Lee Katz, Ph.D. |
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From: kok w. <kok...@gm...> - 2013-08-12 03:57:46
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Wow, that's very great and it's faster than planned. I will certainly try out the pipeline on my genome and update you with the results. I'm thinking of probably having 2/4 evidence will be good enough as false positive is preferred over false negative for the gene prediction, any opinion? Thanks for your efforts and helps. On Sun, Aug 11, 2013 at 7:35 PM, Lee Katz <ls...@gm...> wrote: > Hi Kok, I added a script run_prediction_prodigal.pl into source control. > It outputs a GFF file of CDS predictions. I also made sure it outputs the > training file to the temporary directory because it seems like you are > interested in the training files. > > I also modified run_prediction and the CGPipelineUtils module so that it > predicts alongside the other predictors. Lastly, I added an option > prediction_use_prodigal = 1 under the config file so that you can enable it > for run_prediction. With Prodigal, each gene must have 2/3 or 3/4 majority > to be called (depending on whether you use genemark too). > > I'm new to prodigal, so please let me know if it all looks correct. The > command seems simple enough but I don't know if there are > any idiosyncrasies to be aware of. > > > On Fri, Aug 2, 2013 at 11:32 PM, Gmail <kok...@gm...> wrote: > >> Thanks Jay and Lee. It will be great if the option is added. I like >> prodigal for their better start prediction (from what i get for my test >> genome) and less false prediction for bacterial genome as claimed. Looking >> forward to the update, thanks! >> >> On 02/08/2013, at 23:51, Lee Katz <ls...@gm...> wrote: >> >> I'm returning to the US and back to work on Aug 12. It sounds like a >> worthy addition. >> >> I like prodigal but never bothered to put it in as an option. I think it >> could be something optional like genemark and would be preferred if not >> using genemark. In this way, CGP would still be able to have a majority for >> gene calling even if you don't have genemark. >> >> On Aug 2, 2013, at 15:43, Jay <jhu...@gm...> wrote: >> >> As far as I know, there is no convenient way of doing this. The >> run_prediction script would have to be modified to support running it and >> parsing the results. >> >> On 02/08/2013 22:52, kok wrote: >> >> Is it possible for cg pipeline to include the results of other *ab-initio >> *predictor (eg. prodigal)? Is there any development for this function? >> Or if I would like to use prodigal in place of genemark (if only two >> predictors allowed), can I convert the results of prodigal into >> genemark-like gm_out.lst file for cg pipeline's run_predict as a simple >> modification? >> >> - kok - >> >> >> ------------------------------------------------------------------------------ >> Get your SQL database under version control now! >> Version control is standard for application code, but databases havent >> caught up. So what steps can you take to put your SQL databases under >> version control? Why should you start doing it? Read more to find out.http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >> >> >> >> _______________________________________________ >> Cg-pipeline-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >> >> >> >> ------------------------------------------------------------------------------ >> Get your SQL database under version control now! >> Version control is standard for application code, but databases havent >> caught up. So what steps can you take to put your SQL databases under >> version control? Why should you start doing it? Read more to find out. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >> >> _______________________________________________ >> Cg-pipeline-users mailing list >> Cg-...@li... >> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >> >> > > > -- > Lee Katz, Ph.D. > |
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From: Lee K. <ls...@gm...> - 2013-08-12 11:25:59
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I know! Prodigal is just so easy to use, and so it was really easy to make a wrapper around it. 2/4 might be ok too, but I do not have enough time to perform any rigorous tests to see which way is better. If you have time, please let me and the community know which gives you better results. I think it would be informative to know what 1/4, 2/4, 3/4, and 4/4 gives you for each genome. There is an interesting table that the Georgia Tech compgenomics class created this year, at http://compgenomics2013.biology.gatech.edu/index.php/Gene_Prediction_Group#Gene_Prediction_Pipeline. The way to change the minimum number of predictors is to alter the variable $$settings{min_predictors_to_call_orf} in run_prediction. Around line 161 in run_prediction, where it says something like # Categorize and reconcile predictions Set it back to 2 so that you can have 2/4 predictors. $$settings{min_predictors_to_call_orf}=2; On Sun, Aug 11, 2013 at 11:57 PM, kok wei <kok...@gm...> wrote: > Wow, that's very great and it's faster than planned. I will certainly try > out the pipeline on my genome and update you with the results. I'm thinking > of probably having 2/4 evidence will be good enough as false positive is > preferred over false negative for the gene prediction, any opinion? > > Thanks for your efforts and helps. > > > > On Sun, Aug 11, 2013 at 7:35 PM, Lee Katz <ls...@gm...> wrote: > >> Hi Kok, I added a script run_prediction_prodigal.pl into source control. >> It outputs a GFF file of CDS predictions. I also made sure it outputs the >> training file to the temporary directory because it seems like you are >> interested in the training files. >> >> I also modified run_prediction and the CGPipelineUtils module so that it >> predicts alongside the other predictors. Lastly, I added an option >> prediction_use_prodigal = 1 under the config file so that you can enable it >> for run_prediction. With Prodigal, each gene must have 2/3 or 3/4 majority >> to be called (depending on whether you use genemark too). >> >> I'm new to prodigal, so please let me know if it all looks correct. The >> command seems simple enough but I don't know if there are >> any idiosyncrasies to be aware of. >> >> >> On Fri, Aug 2, 2013 at 11:32 PM, Gmail <kok...@gm...> wrote: >> >>> Thanks Jay and Lee. It will be great if the option is added. I like >>> prodigal for their better start prediction (from what i get for my test >>> genome) and less false prediction for bacterial genome as claimed. Looking >>> forward to the update, thanks! >>> >>> On 02/08/2013, at 23:51, Lee Katz <ls...@gm...> wrote: >>> >>> I'm returning to the US and back to work on Aug 12. It sounds like a >>> worthy addition. >>> >>> I like prodigal but never bothered to put it in as an option. I think >>> it could be something optional like genemark and would be preferred if not >>> using genemark. In this way, CGP would still be able to have a majority for >>> gene calling even if you don't have genemark. >>> >>> On Aug 2, 2013, at 15:43, Jay <jhu...@gm...> wrote: >>> >>> As far as I know, there is no convenient way of doing this. The >>> run_prediction script would have to be modified to support running it and >>> parsing the results. >>> >>> On 02/08/2013 22:52, kok wrote: >>> >>> Is it possible for cg pipeline to include the results of other *ab-initio >>> *predictor (eg. prodigal)? Is there any development for this function? >>> Or if I would like to use prodigal in place of genemark (if only two >>> predictors allowed), can I convert the results of prodigal into >>> genemark-like gm_out.lst file for cg pipeline's run_predict as a simple >>> modification? >>> >>> - kok - >>> >>> >>> ------------------------------------------------------------------------------ >>> Get your SQL database under version control now! >>> Version control is standard for application code, but databases havent >>> caught up. So what steps can you take to put your SQL databases under >>> version control? Why should you start doing it? Read more to find out.http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>> >>> >>> >>> _______________________________________________ >>> Cg-pipeline-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Get your SQL database under version control now! >>> Version control is standard for application code, but databases havent >>> caught up. So what steps can you take to put your SQL databases under >>> version control? Why should you start doing it? Read more to find out. >>> >>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>> >>> _______________________________________________ >>> Cg-pipeline-users mailing list >>> Cg-...@li... >>> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >>> >>> >> >> >> -- >> Lee Katz, Ph.D. >> > > -- Lee Katz, Ph.D. |
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From: kok <kok...@gm...> - 2013-09-30 03:26:49
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Dear Lee Katz, condition evidence CDS w/o prodigal 1 6048 w prodigal 1 8263 w prodigal 2 6192 w prodigal 3 5683 w prodigal 4 875 Table above shows the statistics of the results that I have got for the test on several evidence value. It seems that evidence 2 is the one that I would like to proceed for as it returns with the most CDS which by manual check I can see some are collected from just prodigal and BLAST evidence that missed from previous CGP without prodigal included. However, I find out that the coordinates of the CDS from BLAST and prodigal recorded with infinity "complement(1617923..inf)". From the run_prediction scripts I see that the prodigal is not used for reconcile prediction which I am not sure whether it's the cause of the error, but including prodigal for the start prediction during prediction reconciliation will be good as I have seen cases that prodigal are doing better with the start prediction compared to the other predictors. Hope this is easy to be implemented and thanks for your time. Regards, Kok On 12/8/2013 7:25 PM, Lee Katz wrote: > I know! Prodigal is just so easy to use, and so it was really easy to > make a wrapper around it. > > 2/4 might be ok too, but I do not have enough time to perform any > rigorous tests to see which way is better. If you have time, please > let me and the community know which gives you better results. I think > it would be informative to know what 1/4, 2/4, 3/4, and 4/4 gives you > for each genome. There is an interesting table that the Georgia Tech > compgenomics class created this year, at > http://compgenomics2013.biology.gatech.edu/index.php/Gene_Prediction_Group#Gene_Prediction_Pipeline. > > > The way to change the minimum number of predictors is to alter the > variable $$settings{min_predictors_to_call_orf} in run_prediction. > > Around line 161 in run_prediction, where it says something like > # Categorize and reconcile predictions > Set it back to 2 so that you can have 2/4 predictors. > > $$settings{min_predictors_to_call_orf}=2; > > > On Sun, Aug 11, 2013 at 11:57 PM, kok wei <kok...@gm... > <mailto:kok...@gm...>> wrote: > > Wow, that's very great and it's faster than planned. I will > certainly try out the pipeline on my genome and update you with > the results. I'm thinking of probably having 2/4 evidence will be > good enough as false positive is preferred over false negative for > the gene prediction, any opinion? > > Thanks for your efforts and helps. > > > > On Sun, Aug 11, 2013 at 7:35 PM, Lee Katz <ls...@gm... > <mailto:ls...@gm...>> wrote: > > Hi Kok, I added a script run_prediction_prodigal.pl > <http://run_prediction_prodigal.pl> into source control. It > outputs a GFF file of CDS predictions. I also made sure it > outputs the training file to the temporary directory because > it seems like you are interested in the training files. > > I also modified run_prediction and the CGPipelineUtils module > so that it predicts alongside the other predictors. Lastly, I > added an option prediction_use_prodigal = 1 under the config > file so that you can enable it for run_prediction. With > Prodigal, each gene must have 2/3 or 3/4 majority to be called > (depending on whether you use genemark too). > > I'm new to prodigal, so please let me know if it all looks > correct. The command seems simple enough but I don't know if > there are any idiosyncrasies to be aware of. > > > On Fri, Aug 2, 2013 at 11:32 PM, Gmail <kok...@gm... > <mailto:kok...@gm...>> wrote: > > Thanks Jay and Lee. It will be great if the option is > added. I like prodigal for their better start prediction > (from what i get for my test genome) and less false > prediction for bacterial genome as claimed. Looking > forward to the update, thanks! > > On 02/08/2013, at 23:51, Lee Katz <ls...@gm... > <mailto:ls...@gm...>> wrote: > >> I'm returning to the US and back to work on Aug 12. It >> sounds like a worthy addition. >> >> I like prodigal but never bothered to put it in as an >> option. I think it could be something optional like >> genemark and would be preferred if not using genemark. In >> this way, CGP would still be able to have a majority for >> gene calling even if you don't have genemark. >> >> On Aug 2, 2013, at 15:43, Jay <jhu...@gm... >> <mailto:jhu...@gm...>> wrote: >> >>> As far as I know, there is no convenient way of doing >>> this. The run_prediction script would have to be >>> modified to support running it and parsing the results. >>> >>> On 02/08/2013 22:52, kok wrote: >>>> Is it possible for cg pipeline to include the results >>>> of other /ab-initio /predictor (eg. prodigal)? Is there >>>> any development for this function? >>>> Or if I would like to use prodigal in place of genemark >>>> (if only two predictors allowed), can I convert the >>>> results of prodigal into genemark-like gm_out.lst file >>>> for cg pipeline's run_predict as a simple modification? >>>> >>>> - kok - >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Get your SQL database under version control now! >>>> Version control is standard for application code, but databases havent >>>> caught up. So what steps can you take to put your SQL databases under >>>> version control? Why should you start doing it? Read more to find out. >>>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>>> >>>> >>>> _______________________________________________ >>>> Cg-pipeline-users mailing list >>>> Cg-...@li... <mailto:Cg-...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >>> >>> ------------------------------------------------------------------------------ >>> Get your SQL database under version control now! >>> Version control is standard for application code, but >>> databases havent >>> caught up. So what steps can you take to put your SQL >>> databases under >>> version control? Why should you start doing it? Read >>> more to find out. >>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> Cg-pipeline-users mailing list >>> Cg-...@li... >>> <mailto:Cg-...@li...> >>> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users > > > > > -- > Lee Katz, Ph.D. > > > > > > -- > Lee Katz, Ph.D. |
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From: Lee K. <ls...@gm...> - 2013-10-01 14:12:03
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This looks like something that I need to understand further. Unfortunately I am on furlough and so I am wrapping up everything right now. Please keep this project folder on-hand though because this is a very relevant analysis that will help CG-Pipeline in the future. On Sun, Sep 29, 2013 at 11:26 PM, kok <kok...@gm...> wrote: > Dear Lee Katz, > > condition evidence CDS w/o prodigal 1 6048 w prodigal 1 8263 w > prodigal 2 6192 w prodigal 3 5683 w prodigal 4 875 > Table above shows the statistics of the results that I have got for the > test on several evidence value. It seems that evidence 2 is the one that I > would like to proceed for as it returns with the most CDS which by manual > check I can see some are collected from just prodigal and BLAST evidence > that missed from previous CGP without prodigal included. > > However, I find out that the coordinates of the CDS from BLAST and > prodigal recorded with infinity "complement(1617923..inf)". From the > run_prediction scripts I see that the prodigal is not used for reconcile > prediction which I am not sure whether it's the cause of the error, but > including prodigal for the start prediction during prediction > reconciliation will be good as I have seen cases that prodigal are doing > better with the start prediction compared to the other predictors. Hope > this is easy to be implemented and thanks for your time. > > Regards, > Kok > > > > On 12/8/2013 7:25 PM, Lee Katz wrote: > > I know! Prodigal is just so easy to use, and so it was really easy to > make a wrapper around it. > > 2/4 might be ok too, but I do not have enough time to perform any > rigorous tests to see which way is better. If you have time, please let me > and the community know which gives you better results. I think it would be > informative to know what 1/4, 2/4, 3/4, and 4/4 gives you for each genome. > There is an interesting table that the Georgia Tech compgenomics class > created this year, at > http://compgenomics2013.biology.gatech.edu/index.php/Gene_Prediction_Group#Gene_Prediction_Pipeline. > > > The way to change the minimum number of predictors is to alter the > variable $$settings{min_predictors_to_call_orf} in run_prediction. > > Around line 161 in run_prediction, where it says something like > # Categorize and reconcile predictions > Set it back to 2 so that you can have 2/4 predictors. > > $$settings{min_predictors_to_call_orf}=2; > > > On Sun, Aug 11, 2013 at 11:57 PM, kok wei <kok...@gm...> wrote: > >> Wow, that's very great and it's faster than planned. I will certainly try >> out the pipeline on my genome and update you with the results. I'm thinking >> of probably having 2/4 evidence will be good enough as false positive is >> preferred over false negative for the gene prediction, any opinion? >> >> Thanks for your efforts and helps. >> >> >> >> On Sun, Aug 11, 2013 at 7:35 PM, Lee Katz <ls...@gm...> wrote: >> >>> Hi Kok, I added a script run_prediction_prodigal.pl into source >>> control. It outputs a GFF file of CDS predictions. I also made sure it >>> outputs the training file to the temporary directory because it seems like >>> you are interested in the training files. >>> >>> I also modified run_prediction and the CGPipelineUtils module so that >>> it predicts alongside the other predictors. Lastly, I added an option >>> prediction_use_prodigal = 1 under the config file so that you can enable it >>> for run_prediction. With Prodigal, each gene must have 2/3 or 3/4 majority >>> to be called (depending on whether you use genemark too). >>> >>> I'm new to prodigal, so please let me know if it all looks correct. >>> The command seems simple enough but I don't know if there are >>> any idiosyncrasies to be aware of. >>> >>> >>> On Fri, Aug 2, 2013 at 11:32 PM, Gmail <kok...@gm...> wrote: >>> >>>> Thanks Jay and Lee. It will be great if the option is added. I like >>>> prodigal for their better start prediction (from what i get for my test >>>> genome) and less false prediction for bacterial genome as claimed. Looking >>>> forward to the update, thanks! >>>> >>>> On 02/08/2013, at 23:51, Lee Katz <ls...@gm...> wrote: >>>> >>>> I'm returning to the US and back to work on Aug 12. It sounds like a >>>> worthy addition. >>>> >>>> I like prodigal but never bothered to put it in as an option. I >>>> think it could be something optional like genemark and would be preferred >>>> if not using genemark. In this way, CGP would still be able to have a >>>> majority for gene calling even if you don't have genemark. >>>> >>>> On Aug 2, 2013, at 15:43, Jay <jhu...@gm...> wrote: >>>> >>>> As far as I know, there is no convenient way of doing this. The >>>> run_prediction script would have to be modified to support running it and >>>> parsing the results. >>>> >>>> On 02/08/2013 22:52, kok wrote: >>>> >>>> Is it possible for cg pipeline to include the results of other *ab-initio >>>> *predictor (eg. prodigal)? Is there any development for this function? >>>> Or if I would like to use prodigal in place of genemark (if only two >>>> predictors allowed), can I convert the results of prodigal into >>>> genemark-like gm_out.lst file for cg pipeline's run_predict as a simple >>>> modification? >>>> >>>> - kok - >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Get your SQL database under version control now! >>>> Version control is standard for application code, but databases havent >>>> caught up. So what steps can you take to put your SQL databases under >>>> version control? Why should you start doing it? Read more to find out.http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>>> >>>> >>>> >>>> _______________________________________________ >>>> Cg-pipeline-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Get your SQL database under version control now! >>>> Version control is standard for application code, but databases havent >>>> caught up. So what steps can you take to put your SQL databases under >>>> version control? Why should you start doing it? Read more to find out. >>>> >>>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>>> >>>> _______________________________________________ >>>> Cg-pipeline-users mailing list >>>> Cg-...@li... >>>> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >>>> >>>> >>> >>> >>> -- >>> Lee Katz, Ph.D. >>> >> >> > > > -- > Lee Katz, Ph.D. > > > -- Lee Katz, Ph.D. |
|
From: kok <kok...@gm...> - 2013-10-02 03:25:56
|
Sure, wish the government issue get over soon and everything's fine. Thanks. On 1/10/2013 10:11 PM, Lee Katz wrote: > This looks like something that I need to understand further. > Unfortunately I am on furlough and so I am wrapping up everything > right now. Please keep this project folder on-hand though because > this is a very relevant analysis that will help CG-Pipeline in the future. > > > On Sun, Sep 29, 2013 at 11:26 PM, kok <kok...@gm... > <mailto:kok...@gm...>> wrote: > > Dear Lee Katz, > > condition evidence CDS > w/o prodigal 1 6048 > w prodigal 1 8263 > w prodigal 2 6192 > w prodigal 3 5683 > w prodigal 4 875 > > > Table above shows the statistics of the results that I have got > for the test on several evidence value. It seems that evidence 2 > is the one that I would like to proceed for as it returns with the > most CDS which by manual check I can see some are collected from > just prodigal and BLAST evidence that missed from previous CGP > without prodigal included. > > However, I find out that the coordinates of the CDS from BLAST and > prodigal recorded with infinity "complement(1617923..inf)". From > the run_prediction scripts I see that the prodigal is not used for > reconcile prediction which I am not sure whether it's the cause of > the error, but including prodigal for the start prediction during > prediction reconciliation will be good as I have seen cases that > prodigal are doing better with the start prediction compared to > the other predictors. Hope this is easy to be implemented and > thanks for your time. > > Regards, > Kok > > > > On 12/8/2013 7:25 PM, Lee Katz wrote: >> I know! Prodigal is just so easy to use, and so it was really >> easy to make a wrapper around it. >> >> 2/4 might be ok too, but I do not have enough time to perform any >> rigorous tests to see which way is better. If you have time, >> please let me and the community know which gives you better >> results. I think it would be informative to know what 1/4, 2/4, >> 3/4, and 4/4 gives you for each genome. There is an interesting >> table that the Georgia Tech compgenomics class created this year, >> at >> http://compgenomics2013.biology.gatech.edu/index.php/Gene_Prediction_Group#Gene_Prediction_Pipeline. >> >> >> The way to change the minimum number of predictors is to alter >> the variable $$settings{min_predictors_to_call_orf} in >> run_prediction. >> >> Around line 161 in run_prediction, where it says something like >> # Categorize and reconcile predictions >> Set it back to 2 so that you can have 2/4 predictors. >> >> $$settings{min_predictors_to_call_orf}=2; >> >> >> On Sun, Aug 11, 2013 at 11:57 PM, kok wei <kok...@gm... >> <mailto:kok...@gm...>> wrote: >> >> Wow, that's very great and it's faster than planned. I will >> certainly try out the pipeline on my genome and update you >> with the results. I'm thinking of probably having 2/4 >> evidence will be good enough as false positive is preferred >> over false negative for the gene prediction, any opinion? >> >> Thanks for your efforts and helps. >> >> >> >> On Sun, Aug 11, 2013 at 7:35 PM, Lee Katz <ls...@gm... >> <mailto:ls...@gm...>> wrote: >> >> Hi Kok, I added a script run_prediction_prodigal.pl >> <http://run_prediction_prodigal.pl> into source control. >> It outputs a GFF file of CDS predictions. I also made >> sure it outputs the training file to the temporary >> directory because it seems like you are interested in the >> training files. >> >> I also modified run_prediction and the CGPipelineUtils >> module so that it predicts alongside the other >> predictors. Lastly, I added an option >> prediction_use_prodigal = 1 under the config file so that >> you can enable it for run_prediction. With Prodigal, >> each gene must have 2/3 or 3/4 majority to be called >> (depending on whether you use genemark too). >> >> I'm new to prodigal, so please let me know if it all >> looks correct. The command seems simple enough but I >> don't know if there are any idiosyncrasies to be aware of. >> >> >> On Fri, Aug 2, 2013 at 11:32 PM, Gmail >> <kok...@gm... <mailto:kok...@gm...>> wrote: >> >> Thanks Jay and Lee. It will be great if the option is >> added. I like prodigal for their better start >> prediction (from what i get for my test genome) and >> less false prediction for bacterial genome as >> claimed. Looking forward to the update, thanks! >> >> On 02/08/2013, at 23:51, Lee Katz <ls...@gm... >> <mailto:ls...@gm...>> wrote: >> >>> I'm returning to the US and back to work on Aug 12. >>> It sounds like a worthy addition. >>> >>> I like prodigal but never bothered to put it in as >>> an option. I think it could be something optional >>> like genemark and would be preferred if not using >>> genemark. In this way, CGP would still be able to >>> have a majority for gene calling even if you don't >>> have genemark. >>> >>> On Aug 2, 2013, at 15:43, Jay <jhu...@gm... >>> <mailto:jhu...@gm...>> wrote: >>> >>>> As far as I know, there is no convenient way of >>>> doing this. The run_prediction script would have to >>>> be modified to support running it and parsing the >>>> results. >>>> >>>> On 02/08/2013 22:52, kok wrote: >>>>> Is it possible for cg pipeline to include the >>>>> results of other /ab-initio /predictor (eg. >>>>> prodigal)? Is there any development for this >>>>> function? >>>>> Or if I would like to use prodigal in place of >>>>> genemark (if only two predictors allowed), can I >>>>> convert the results of prodigal into genemark-like >>>>> gm_out.lst file for cg pipeline's run_predict as a >>>>> simple modification? >>>>> >>>>> - kok - >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Get your SQL database under version control now! >>>>> Version control is standard for application code, but databases havent >>>>> caught up. So what steps can you take to put your SQL databases under >>>>> version control? Why should you start doing it? Read more to find out. >>>>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>>>> >>>>> >>>>> _______________________________________________ >>>>> Cg-pipeline-users mailing list >>>>> Cg-...@li... <mailto:Cg-...@li...> >>>>> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >>>> >>>> ------------------------------------------------------------------------------ >>>> Get your SQL database under version control now! >>>> Version control is standard for application code, >>>> but databases havent >>>> caught up. So what steps can you take to put your >>>> SQL databases under >>>> version control? Why should you start doing it? >>>> Read more to find out. >>>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>>> _______________________________________________ >>>> Cg-pipeline-users mailing list >>>> Cg-...@li... >>>> <mailto:Cg-...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >> >> >> >> >> -- >> Lee Katz, Ph.D. >> >> >> >> >> >> -- >> Lee Katz, Ph.D. > > > > > -- > Lee Katz, Ph.D. |
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From: Lee K. <ls...@gm...> - 2014-03-19 18:05:02
|
Hi Kok, I am revisiting this issue right now. I am trying gene prediction on a plasmid that we have in-house because it is faster to do so. My table looks like the following: conditionevidenceCDS w/o prodigal1194 w prodigal1203 w prodigal2178w prodigal3164 w prodigal45 So using all four predictors is ridiculous (not that anyone was suggesting that). I also agree that two predictors is sufficient and is in line with what I expected. I'll add that as a default option in the conf file in cgpipelinerc. The option will be listed as prediction_min_predictors_to_call_orf = 2 I know it has been a long time, but did I answer the whole issue? On Tue, Oct 1, 2013 at 10:11 AM, Lee Katz <ls...@gm...> wrote: > This looks like something that I need to understand further. > Unfortunately I am on furlough and so I am wrapping up everything right > now. Please keep this project folder on-hand though because this is a very > relevant analysis that will help CG-Pipeline in the future. > > > On Sun, Sep 29, 2013 at 11:26 PM, kok <kok...@gm...> wrote: > >> Dear Lee Katz, >> >> condition evidence CDS w/o prodigal 1 6048 w prodigal 1 8263 w >> prodigal 2 6192 w prodigal 3 5683 w prodigal 4 875 >> Table above shows the statistics of the results that I have got for the >> test on several evidence value. It seems that evidence 2 is the one that I >> would like to proceed for as it returns with the most CDS which by manual >> check I can see some are collected from just prodigal and BLAST evidence >> that missed from previous CGP without prodigal included. >> >> However, I find out that the coordinates of the CDS from BLAST and >> prodigal recorded with infinity "complement(1617923..inf)". From the >> run_prediction scripts I see that the prodigal is not used for reconcile >> prediction which I am not sure whether it's the cause of the error, but >> including prodigal for the start prediction during prediction >> reconciliation will be good as I have seen cases that prodigal are doing >> better with the start prediction compared to the other predictors. Hope >> this is easy to be implemented and thanks for your time. >> >> Regards, >> Kok >> >> >> >> On 12/8/2013 7:25 PM, Lee Katz wrote: >> >> I know! Prodigal is just so easy to use, and so it was really easy to >> make a wrapper around it. >> >> 2/4 might be ok too, but I do not have enough time to perform any >> rigorous tests to see which way is better. If you have time, please let me >> and the community know which gives you better results. I think it would be >> informative to know what 1/4, 2/4, 3/4, and 4/4 gives you for each genome. >> There is an interesting table that the Georgia Tech compgenomics class >> created this year, at >> http://compgenomics2013.biology.gatech.edu/index.php/Gene_Prediction_Group#Gene_Prediction_Pipeline. >> >> >> The way to change the minimum number of predictors is to alter the >> variable $$settings{min_predictors_to_call_orf} in run_prediction. >> >> Around line 161 in run_prediction, where it says something like >> # Categorize and reconcile predictions >> Set it back to 2 so that you can have 2/4 predictors. >> >> $$settings{min_predictors_to_call_orf}=2; >> >> >> On Sun, Aug 11, 2013 at 11:57 PM, kok wei <kok...@gm...> wrote: >> >>> Wow, that's very great and it's faster than planned. I will certainly >>> try out the pipeline on my genome and update you with the results. I'm >>> thinking of probably having 2/4 evidence will be good enough as false >>> positive is preferred over false negative for the gene prediction, any >>> opinion? >>> >>> Thanks for your efforts and helps. >>> >>> >>> >>> On Sun, Aug 11, 2013 at 7:35 PM, Lee Katz <ls...@gm...> wrote: >>> >>>> Hi Kok, I added a script run_prediction_prodigal.pl into source >>>> control. It outputs a GFF file of CDS predictions. I also made sure it >>>> outputs the training file to the temporary directory because it seems like >>>> you are interested in the training files. >>>> >>>> I also modified run_prediction and the CGPipelineUtils module so that >>>> it predicts alongside the other predictors. Lastly, I added an option >>>> prediction_use_prodigal = 1 under the config file so that you can enable it >>>> for run_prediction. With Prodigal, each gene must have 2/3 or 3/4 majority >>>> to be called (depending on whether you use genemark too). >>>> >>>> I'm new to prodigal, so please let me know if it all looks correct. >>>> The command seems simple enough but I don't know if there are >>>> any idiosyncrasies to be aware of. >>>> >>>> >>>> On Fri, Aug 2, 2013 at 11:32 PM, Gmail <kok...@gm...> wrote: >>>> >>>>> Thanks Jay and Lee. It will be great if the option is added. I like >>>>> prodigal for their better start prediction (from what i get for my test >>>>> genome) and less false prediction for bacterial genome as claimed. Looking >>>>> forward to the update, thanks! >>>>> >>>>> On 02/08/2013, at 23:51, Lee Katz <ls...@gm...> wrote: >>>>> >>>>> I'm returning to the US and back to work on Aug 12. It sounds like >>>>> a worthy addition. >>>>> >>>>> I like prodigal but never bothered to put it in as an option. I >>>>> think it could be something optional like genemark and would be preferred >>>>> if not using genemark. In this way, CGP would still be able to have a >>>>> majority for gene calling even if you don't have genemark. >>>>> >>>>> On Aug 2, 2013, at 15:43, Jay <jhu...@gm...> wrote: >>>>> >>>>> As far as I know, there is no convenient way of doing this. The >>>>> run_prediction script would have to be modified to support running it and >>>>> parsing the results. >>>>> >>>>> On 02/08/2013 22:52, kok wrote: >>>>> >>>>> Is it possible for cg pipeline to include the results of other *ab-initio >>>>> *predictor (eg. prodigal)? Is there any development for this >>>>> function? >>>>> Or if I would like to use prodigal in place of genemark (if only two >>>>> predictors allowed), can I convert the results of prodigal into >>>>> genemark-like gm_out.lst file for cg pipeline's run_predict as a simple >>>>> modification? >>>>> >>>>> - kok - >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Get your SQL database under version control now! >>>>> Version control is standard for application code, but databases havent >>>>> caught up. So what steps can you take to put your SQL databases under >>>>> version control? Why should you start doing it? Read more to find out.http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Cg-pipeline-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Get your SQL database under version control now! >>>>> Version control is standard for application code, but databases havent >>>>> caught up. So what steps can you take to put your SQL databases under >>>>> version control? Why should you start doing it? Read more to find out. >>>>> >>>>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>>>> >>>>> _______________________________________________ >>>>> Cg-pipeline-users mailing list >>>>> Cg-...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >>>>> >>>>> >>>> >>>> >>>> -- >>>> Lee Katz, Ph.D. >>>> >>> >>> >> >> >> -- >> Lee Katz, Ph.D. >> >> >> > > > -- > Lee Katz, Ph.D. > -- Lee Katz, Ph.D. |
|
From: kok <kok...@gm...> - 2014-03-25 04:05:30
|
Dear Lee Katz, Thanks for revisiting the issue. I did changed the option in the conf file previously during my test but another issue I pointed out was the coordinates of the CDS from only BLAST and prodigal recorded with infinity coordinate "complement(1617923..inf)". From the run_prediction scripts I see that the prodigal is not used for reconcile prediction which I am not sure whether it's the cause of the error (or maybe you have changed this as well?). Hope you get what I mean here and thanks for your time again. - kok - > Hi Kok, I am revisiting this issue right now. I am trying gene > prediction on a plasmid that we have in-house because it is faster to > do so. My table looks like the following: > > condition evidence CDS > w/o prodigal 1 194 > w prodigal 1 203 > w prodigal 2 178 > w prodigal 3 164 > w prodigal 4 5 > > > So using all four predictors is ridiculous (not that anyone was > suggesting that). I also agree that two predictors is sufficient and > is in line with what I expected. I'll add that as a default option in > the conf file in cgpipelinerc. The option will be listed as > > prediction_min_predictors_to_call_orf = 2 > > I know it has been a long time, but did I answer the whole issue? > > > > On Tue, Oct 1, 2013 at 10:11 AM, Lee Katz <ls...@gm... > <mailto:ls...@gm...>> wrote: > > This looks like something that I need to understand further. > Unfortunately I am on furlough and so I am wrapping up everything > right now. Please keep this project folder on-hand though because > this is a very relevant analysis that will help CG-Pipeline in the > future. > > > On Sun, Sep 29, 2013 at 11:26 PM, kok <kok...@gm... > <mailto:kok...@gm...>> wrote: > > Dear Lee Katz, > > condition evidence CDS > w/o prodigal 1 6048 > w prodigal 1 8263 > w prodigal 2 6192 > w prodigal 3 5683 > w prodigal 4 875 > > > Table above shows the statistics of the results that I have > got for the test on several evidence value. It seems that > evidence 2 is the one that I would like to proceed for as it > returns with the most CDS which by manual check I can see some > are collected from just prodigal and BLAST evidence that > missed from previous CGP without prodigal included. > > However, I find out that the coordinates of the CDS from BLAST > and prodigal recorded with infinity > "complement(1617923..inf)". From the run_prediction scripts I > see that the prodigal is not used for reconcile prediction > which I am not sure whether it's the cause of the error, but > including prodigal for the start prediction during prediction > reconciliation will be good as I have seen cases that prodigal > are doing better with the start prediction compared to the > other predictors. Hope this is easy to be implemented and > thanks for your time. > > Regards, > Kok > > > > On 12/8/2013 7:25 PM, Lee Katz wrote: >> I know! Prodigal is just so easy to use, and so it was >> really easy to make a wrapper around it. >> >> 2/4 might be ok too, but I do not have enough time to perform >> any rigorous tests to see which way is better. If you have >> time, please let me and the community know which gives you >> better results. I think it would be informative to know what >> 1/4, 2/4, 3/4, and 4/4 gives you for each genome. There is >> an interesting table that the Georgia Tech compgenomics class >> created this year, at >> http://compgenomics2013.biology.gatech.edu/index.php/Gene_Prediction_Group#Gene_Prediction_Pipeline. >> >> >> The way to change the minimum number of predictors is to >> alter the variable $$settings{min_predictors_to_call_orf} in >> run_prediction. >> >> Around line 161 in run_prediction, where it says something like >> # Categorize and reconcile predictions >> Set it back to 2 so that you can have 2/4 predictors. >> >> $$settings{min_predictors_to_call_orf}=2; >> >> >> On Sun, Aug 11, 2013 at 11:57 PM, kok wei <kok...@gm... >> <mailto:kok...@gm...>> wrote: >> >> Wow, that's very great and it's faster than planned. I >> will certainly try out the pipeline on my genome and >> update you with the results. I'm thinking of probably >> having 2/4 evidence will be good enough as false positive >> is preferred over false negative for the gene prediction, >> any opinion? >> >> Thanks for your efforts and helps. >> >> >> >> On Sun, Aug 11, 2013 at 7:35 PM, Lee Katz >> <ls...@gm... <mailto:ls...@gm...>> wrote: >> >> Hi Kok, I added a script run_prediction_prodigal.pl >> <http://run_prediction_prodigal.pl> into source >> control. It outputs a GFF file of CDS predictions. >> I also made sure it outputs the training file to the >> temporary directory because it seems like you are >> interested in the training files. >> >> I also modified run_prediction and the >> CGPipelineUtils module so that it predicts alongside >> the other predictors. Lastly, I added an option >> prediction_use_prodigal = 1 under the config file so >> that you can enable it for run_prediction. With >> Prodigal, each gene must have 2/3 or 3/4 majority to >> be called (depending on whether you use genemark too). >> >> I'm new to prodigal, so please let me know if it all >> looks correct. The command seems simple enough but I >> don't know if there are any idiosyncrasies to be >> aware of. >> >> >> On Fri, Aug 2, 2013 at 11:32 PM, Gmail >> <kok...@gm... <mailto:kok...@gm...>> wrote: >> >> Thanks Jay and Lee. It will be great if the >> option is added. I like prodigal for their better >> start prediction (from what i get for my test >> genome) and less false prediction for bacterial >> genome as claimed. Looking forward to the update, >> thanks! >> >> On 02/08/2013, at 23:51, Lee Katz >> <ls...@gm... <mailto:ls...@gm...>> wrote: >> >>> I'm returning to the US and back to work on Aug >>> 12. It sounds like a worthy addition. >>> >>> I like prodigal but never bothered to put it in >>> as an option. I think it could be something >>> optional like genemark and would be preferred if >>> not using genemark. In this way, CGP would still >>> be able to have a majority for gene calling even >>> if you don't have genemark. >>> >>> On Aug 2, 2013, at 15:43, Jay >>> <jhu...@gm... >>> <mailto:jhu...@gm...>> wrote: >>> >>>> As far as I know, there is no convenient way of >>>> doing this. The run_prediction script would >>>> have to be modified to support running it and >>>> parsing the results. >>>> >>>> On 02/08/2013 22:52, kok wrote: >>>>> Is it possible for cg pipeline to include the >>>>> results of other /ab-initio /predictor (eg. >>>>> prodigal)? Is there any development for this >>>>> function? >>>>> Or if I would like to use prodigal in place of >>>>> genemark (if only two predictors allowed), can >>>>> I convert the results of prodigal into >>>>> genemark-like gm_out.lst file for cg >>>>> pipeline's run_predict as a simple modification? >>>>> >>>>> - kok - >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Get your SQL database under version control now! >>>>> Version control is standard for application code, but databases havent >>>>> caught up. So what steps can you take to put your SQL databases under >>>>> version control? Why should you start doing it? Read more to find out. >>>>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>>>> >>>>> >>>>> _______________________________________________ >>>>> Cg-pipeline-users mailing list >>>>> Cg-...@li... <mailto:Cg-...@li...> >>>>> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >>>> >>>> ------------------------------------------------------------------------------ >>>> Get your SQL database under version control now! >>>> Version control is standard for application >>>> code, but databases havent >>>> caught up. So what steps can you take to put >>>> your SQL databases under >>>> version control? Why should you start doing it? >>>> Read more to find out. >>>> http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk >>>> _______________________________________________ >>>> Cg-pipeline-users mailing list >>>> Cg-...@li... >>>> <mailto:Cg-...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users >> >> >> >> >> -- >> Lee Katz, Ph.D. >> >> >> >> >> >> -- >> Lee Katz, Ph.D. > > > > > -- > Lee Katz, Ph.D. > > > > > -- > Lee Katz, Ph.D. |
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