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From: Scott C. <ca...@cs...> - 2003-04-25 13:53:08
|
Charles, Another thing that occurred to me for debugging this: turn on query logging for postgres so you can see what query is being generated to find the landmark. To turn on query logging for postgres, as either root or postgres, edit the postgres.conf file (I think it is typically in /var/lib/pgsql) and set log_pid and log_statement equal to true (you can also set log_duration to get the time elapsed on the queries). Then restart postgres. Then the queries will be logged in /var/log/messages. Don't forget to turn logging off after you finished debugging, as it does slow things down (an makes messages grow to an incredible size) if you don't. Scott On Thu, 2003-04-24 at 15:44, Scott Cain wrote: > I've seen "landmark not recognized" on a fairly regular basis, so you > would think that I would remember how to fix it by now. Since I can't > think of much (a single pathetic guess below), I've cc'd this to the > gbrowse email list, so someone can remind both of us. > > <grasping_at_straws>Is it possible that there is a trailing space in > either the database or the webbased query? I believe the gbrowse will > trim off trailing white space in the form, but what if there is trailing > white space in the database? > </grasping_at_straws> > > That's all I can think of right now. > > Scott > > On Thu, 2003-04-24 at 15:32, Charles Hauser wrote: > > On Thu, 2003-04-24 at 15:20, Scott Cain wrote: > > > Is the landmark not recognized error coming from a chado or gff backend > > > gbrowse? > > > > sorry, GFF backend in pg. > > > > I was just checking the data and all the tables appear ok, and 'Cp' is > > fref: > > > > chlamy=>select * from fdata where fid=1; > > fid | fref | fstart | fstop | fbin | ftypeid | fscore | fstrand | fphase | gid | ftarget_start | ftarget_stop > > -----+------+--------+--------+---------------+---------+--------+---------+--------+-----+---------------+-------------- > > 1 | Cp | 1 | 203395 | 1000000 | 1 | | + | | 1 | > > > > > > I loaded the data : > > perl load_gff.pl -adaptor dbi::pg -upgrade -d chlamy -f > > ~/CHADO/BK000554.fa.gz ~/SCRIPTS/EXONERATE/BK000554.gff > > > > > > > > > > [GENERAL] > > description = C. reinhardtii > > user = nobody > > pass = > > adaptor = dbi::pg > > database = chlamy > > > > > > > > chlamy=>\du > > List of database users > > User name | User ID | Attributes > > -----------+---------+---------------------------- > > chauser | x | superuser, create database > > nobody | xxx| > > > > > > > > > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
|
From: Scott C. <ca...@cs...> - 2003-04-24 20:30:44
|
Lincoln, I think I've found a bug in gff parsing and/or importation into mysql (depending on your point of view). I have the following line human_chr01.gff from the gmod website: Chr1 NCBI component 2544887 2724565 . ? . Sequence "AL592464.14"; Name "AL592464.14" Note the '?' in strand's place. When importing into mysql, it quietly converts it to a ' ' (a single space, which is not a NULL). When trying to import into postgres, the '?' remains in the INSERT statement and it fails to import because there is a check constraint on fstrand that it must either be '+', '-', or NULL. So, is it mysql's fault for silently converting (seems likely), or should the parser convert '?' to a NULL (which seems like a reasonable thing to do, but I don't know if it is in the spec)? Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
|
From: Scott C. <ca...@cs...> - 2003-04-24 19:44:30
|
I've seen "landmark not recognized" on a fairly regular basis, so you would think that I would remember how to fix it by now. Since I can't think of much (a single pathetic guess below), I've cc'd this to the gbrowse email list, so someone can remind both of us. <grasping_at_straws>Is it possible that there is a trailing space in either the database or the webbased query? I believe the gbrowse will trim off trailing white space in the form, but what if there is trailing white space in the database? </grasping_at_straws> That's all I can think of right now. Scott On Thu, 2003-04-24 at 15:32, Charles Hauser wrote: > On Thu, 2003-04-24 at 15:20, Scott Cain wrote: > > Is the landmark not recognized error coming from a chado or gff backend > > gbrowse? > > sorry, GFF backend in pg. > > I was just checking the data and all the tables appear ok, and 'Cp' is > fref: > > chlamy=>select * from fdata where fid=1; > fid | fref | fstart | fstop | fbin | ftypeid | fscore | fstrand | fphase | gid | ftarget_start | ftarget_stop > -----+------+--------+--------+---------------+---------+--------+---------+--------+-----+---------------+-------------- > 1 | Cp | 1 | 203395 | 1000000 | 1 | | + | | 1 | > > > I loaded the data : > perl load_gff.pl -adaptor dbi::pg -upgrade -d chlamy -f > ~/CHADO/BK000554.fa.gz ~/SCRIPTS/EXONERATE/BK000554.gff > > > > > [GENERAL] > description = C. reinhardtii > user = nobody > pass = > adaptor = dbi::pg > database = chlamy > > > > chlamy=>\du > List of database users > User name | User ID | Attributes > -----------+---------+---------------------------- > chauser | x | superuser, create database > nobody | xxx| > > > > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
|
From: Lincoln S. <ls...@cs...> - 2003-04-23 21:02:35
|
Hi Gavin, It looks great! I'm very happy that gbrowse has worked for you. Your=20 contributions to bioperl would be very much appreciated, and if you like = you=20 can simply send me a patch file (against a recent version of bioperl), an= d I=20 will put them into CVS. Could you briefly summarize what features you've added? I'm unfamiliar w= ith=20 the BDGAd/postgres adaptor, but it sounds like I should know about it. Lincoln On Monday 21 April 2003 11:00 am, Gavin Duggan wrote: > Hello Dr Stein, > > I've been lurking on the bioperl and gmod discussion for a while now, b= ut > I thought I'd let you know that we recently used Gbrowse as one of the > pillars for our analysis and presentation of the Chromosome 7 project h= ere > at TCAG. The results are at www.chr7.org. > > We put both gbrowse and the relevant parts of Bioperl through a fairly > good workout on the full 158 Mb Annotation (which comprises a lot of > tracks) and it's performed well, both from a user standpoint and as an > open-source (and hence tweakable) tool. Many thanks to you and the who= le > GMOD team. > > Now that things have slowed down I'll try to submit some of the bioperl > patch work we've done here back to the project. (The BDGAd/postgres > adaptor in particular, if you think it would be of use to others. I've > fallen behind on the list and can't remember if the new schemas will > become prevalent shortly as the gbrowse backend). > > Thanks again, > > Gavin Duggan - H.BMath CompSci/H.BSc (Molecular Biology) - UWaterloo > Bioinformatics Hacker - The Center for Applied Genomics - Toronto --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
|
From: Lincoln S. <ls...@cs...> - 2003-04-17 18:03:23
|
> > If you CVS update to the latest bioperl-live the problem will go away= =2E > > Can I just re-install the module(s) that were changed? I'd prefer not t= o > use all of bioperl-live. Which module(s) were changed? You could reinstall everything under Bio/DB/GFF, but I can't guarantee th= at=20 just updating that section will be coherent with the rest of the dist=20 ribution. > I've tried 16 & 21bp oligos (from coding and intergenic regions) in upp= er > and lowercase, but nothing works. And there's no message in the error l= og. Silly question, but is the DNA loaded in your database? Lincoln --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
|
From: <ko...@sf...> - 2003-04-17 16:14:11
|
On Thu, 17 Apr 2003 09:20:58 -0400 ls...@cs... wrote: > > > And the EMBL dumper doesn't work > > in either browser. I get this error message in the log: > > > > MSG: Abstract method "Bio::SeqI::primary_seq" is not implemented by > package > Bio::DB::GFF::RelSegment. > > There was a change in bioperl that I didn't track before the 1.2.1 release. > If you CVS update to the latest bioperl-live the problem will go away. Can I just re-install the module(s) that were changed? I'd prefer not to use all of bioperl-live. Which module(s) were changed? > > Also, the oligo-searching function doesn't work. It keeps coming up > > "landmark not recognized". I vaguely remember it working in the 1.49 > > version of GBrowse. Now I'm using v1.50 and bioperl 1.2.1. > > It's still working for me. There's a size limit of 15 bp: have you tested a > sufficiently long oligo that you know should be found? This may also turn > out to be a case-sensitivity issue. Is the DNA you're loading in upper or > lowercase? I've tried 16 & 21bp oligos (from coding and intergenic regions) in upper and lowercase, but nothing works. And there's no message in the error log. Thanks for your help, Korine |
|
From: Lincoln S. <ls...@cs...> - 2003-04-17 13:21:35
|
> I've asked this question before, but I'm still having trouble with the > sequence dumpers. The GAME and BSML formats seem to work in Netscape, b= ut > they don't show up in Internet Explorer.=20 Internet Explorer tries to parse and display the XML output. Selecting "= text"=20 output should force the output to be displayed as plain text, but it isn'= t=20 working when I try it. I will try to fix this today. > And the EMBL dumper doesn't work > in either browser. I get this error message in the log: > > MSG: Abstract method "Bio::SeqI::primary_seq" is not implemented by pac= kage > Bio::DB::GFF::RelSegment. There was a change in bioperl that I didn't track before the 1.2.1 releas= e. =20 If you CVS update to the latest bioperl-live the problem will go away. > Also, the oligo-searching function doesn't work. It keeps coming up > "landmark not recognized". I vaguely remember it working in the 1.49 > version of GBrowse. Now I'm using v1.50 and bioperl 1.2.1. It's still working for me. There's a size limit of 15 bp: have you teste= d a=20 sufficiently long oligo that you know should be found? This may also tur= n=20 out to be a case-sensitivity issue. Is the DNA you're loading in upper = or=20 lowercase? Lincoln > > Thanks in advance to anyone who can help me. > > Korine > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > Korine Ung > Site Administrator/Laboratory Assistant > Brinkman Laboratory > Department of Molecular Biology and Biochemistry > Simon Fraser University > Tel: 604-291-5414 > Email: ko...@sf... > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
|
From: <ko...@sf...> - 2003-04-15 22:58:36
|
Hi, I've asked this question before, but I'm still having trouble with the sequence dumpers. The GAME and BSML formats seem to work in Netscape, but they don't show up in Internet Explorer. And the EMBL dumper doesn't work in either browser. I get this error message in the log: MSG: Abstract method "Bio::SeqI::primary_seq" is not implemented by package Bio::DB::GFF::RelSegment. Also, the oligo-searching function doesn't work. It keeps coming up "landmark not recognized". I vaguely remember it working in the 1.49 version of GBrowse. Now I'm using v1.50 and bioperl 1.2.1. Thanks in advance to anyone who can help me. Korine ======================== Korine Ung Site Administrator/Laboratory Assistant Brinkman Laboratory Department of Molecular Biology and Biochemistry Simon Fraser University Tel: 604-291-5414 Email: ko...@sf... |
|
From: Lincoln S. <ls...@cs...> - 2003-04-15 21:50:13
|
Hi Charles, When the number of features becomes too high in any one track, gbrowse will automatically turn off bumping unless the user explicitly turns it on. You can control that threshold with the "bump density" option in the [GENERAL] section. Set the number to a very high number if you never want bumping to occur. Lincoln On Monday 14 April 2003 05:39 pm, Charles Hauser wrote: > All, > > Question about feature density GBrowse can display. > > I have loaded ESTs mapped to a scaffold (exonerate) and GeneMark > predictions. > > I think I have too mant ESTs to display. > > If I set browser to display: > - scaffold_688:15900-16900 > ->OK, ends of ~ 30 ESTs & genemark prediction segment displayed > > - bump to right 500 bp: > -> ESTs collapse into single icon/line > > I've undoubtedly crossed a threshhold of feature display. > > -> use semantic zooming to make icons smaller if density is high? > > Charles > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- Lincoln Stein ls...@cs... Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) |
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From: Charles H. <ch...@du...> - 2003-04-14 21:39:20
|
All, Question about feature density GBrowse can display. I have loaded ESTs mapped to a scaffold (exonerate) and GeneMark predictions. I think I have too mant ESTs to display. If I set browser to display: - scaffold_688:15900-16900 ->OK, ends of ~ 30 ESTs & genemark prediction segment displayed - bump to right 500 bp: -> ESTs collapse into single icon/line I've undoubtedly crossed a threshhold of feature display. -> use semantic zooming to make icons smaller if density is high? Charles |
|
From: Lincoln S. <ls...@cs...> - 2003-04-14 19:33:12
|
Hi Charles,
The order isn't important. You can print the gene_model line AFTER all t=
he=20
internal component lines. When the GFF is loaded, the database will take=
=20
care of the rest.
I apologize if the docs made it seem as though there is a particular requ=
ired=20
order. Indeed, you don't even have to put the various components togeth=
er=20
but can interleaf them with other gene models.
Lincoln
On Monday 14 April 2003 12:07 pm, Charles Hauser wrote:
> All,
>
> I'd like to build an aggregator to display GeneMark predicted gene
> models for a scaffold.
>
> I need to add a line to the gff file prior to the details for each mode=
l
> designating a method 'gene_model' and the range InternalExon ->
> TerminalExon:
>
> such as:
> scaffold_688=09Genemark.hmm.eu=09gene_model=0954=092567=09.=09+=09.
>
> and then create an aggregator:
> =09model{InternalExon,TerminalExon/gene_model}
>
>
> Problem is, as currently implemented, the script can't print such a lin=
e
> prior to the details as the end of the TerminalExon is not known.
>
> Is the only solution to:
> - gather up all the details for each model,
> - find start (1st InternalExon) '54'
> - find stop (TerminalExon) '2567'
> - print gff
>
> Or is there a better way to display these data?
>
> Charles
>
>
> data from script:
>
> scaffold_688=09Genemark.hmm.eu=09InternalExon=0954=09161=09.=09+=09.
> scaffold_688=09Genemark.hmm.eu=09InternalExon=09632=09742=09.=09+=09.
> scaffold_688=09Genemark.hmm.eu=09InternalExon=092059=092267=09.=09+=09.
> scaffold_688=09Genemark.hmm.eu=09TerminalExon=092534=092567=09.=09+=09.
>
>
> my $Genemark =3D Bio::Tools::Genemark->new(-file =3D> $infile);
>
> while(my $gene =3D $Genemark->next_prediction()) {
> my @exon_arr =3D $gene->exons();
> foreach my $feat (@exon_arr) {
> =09 my @tags =3D $feat->get_all_tags();
> =09 $feat->seq_id($scaffold);
> =09 $gffout->write_feature($feat);
> }
> }
>
>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
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> Gmo...@li...
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--=20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Lincoln D. Stein Cold Spring Harbor Laboratory
ls...@cs...=09=09=09 Cold Spring Harbor, NY
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
|
|
From: Charles H. <ch...@du...> - 2003-04-14 16:08:30
|
All,
I'd like to build an aggregator to display GeneMark predicted gene
models for a scaffold.
I need to add a line to the gff file prior to the details for each model
designating a method 'gene_model' and the range InternalExon ->
TerminalExon:
such as:
scaffold_688 Genemark.hmm.eu gene_model 54 2567 . + .
and then create an aggregator:
model{InternalExon,TerminalExon/gene_model}
Problem is, as currently implemented, the script can't print such a line
prior to the details as the end of the TerminalExon is not known.
Is the only solution to:
- gather up all the details for each model,
- find start (1st InternalExon) '54'
- find stop (TerminalExon) '2567'
- print gff
Or is there a better way to display these data?
Charles
data from script:
scaffold_688 Genemark.hmm.eu InternalExon 54 161 . + .
scaffold_688 Genemark.hmm.eu InternalExon 632 742 . + .
scaffold_688 Genemark.hmm.eu InternalExon 2059 2267 . + .
scaffold_688 Genemark.hmm.eu TerminalExon 2534 2567 . + .
my $Genemark = Bio::Tools::Genemark->new(-file => $infile);
while(my $gene = $Genemark->next_prediction()) {
my @exon_arr = $gene->exons();
foreach my $feat (@exon_arr) {
my @tags = $feat->get_all_tags();
$feat->seq_id($scaffold);
$gffout->write_feature($feat);
}
}
|
|
From: Scott C. <ca...@cs...> - 2003-04-11 18:30:15
|
No, although to be honest, I usually don't look that closely at the translation picture--I usually just include it for stress testing. The picture just jumped out at me when it looked that way. I have looked at the zoomed in translations (so that I could see residues) and it got those right. Scott On Fri, 2003-04-11 at 14:25, Lincoln Stein wrote: > Hi Scott, > > I think it's a clip error. The problem is manifesting at the very end of the > chromosome. Do you see this occurring elsewhere? > > Lincoln > > On Friday 11 April 2003 01:35 pm, Scott Cain wrote: > > Lincoln, > > > > Take a look at the link below. I suspect this is indicative of a bug in > > how the translations are handled (specifically, something with the > > reverse translation being displayed in the wrong direction). What do > > you think? > > > > http://www.wormbase.org/db/seq/gbrowse?name=IV%3A17482291..17502290;source= > >wormbase;width=800;label=CG-TranslationF-DNA%2FGC%20Content-TranslationR > > > > Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
|
From: Lincoln S. <ls...@cs...> - 2003-04-11 18:25:45
|
Hi Scott, I think it's a clip error. The problem is manifesting at the very end of= the=20 chromosome. Do you see this occurring elsewhere? Lincoln On Friday 11 April 2003 01:35 pm, Scott Cain wrote: > Lincoln, > > Take a look at the link below. I suspect this is indicative of a bug i= n > how the translations are handled (specifically, something with the > reverse translation being displayed in the wrong direction). What do > you think? > > http://www.wormbase.org/db/seq/gbrowse?name=3DIV%3A17482291..17502290;s= ource=3D >wormbase;width=3D800;label=3DCG-TranslationF-DNA%2FGC%20Content-Translat= ionR > > Scott --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
|
From: Scott C. <ca...@cs...> - 2003-04-11 17:35:59
|
Lincoln, Take a look at the link below. I suspect this is indicative of a bug in how the translations are handled (specifically, something with the reverse translation being displayed in the wrong direction). What do you think? http://www.wormbase.org/db/seq/gbrowse?name=IV%3A17482291..17502290;source=wormbase;width=800;label=CG-TranslationF-DNA%2FGC%20Content-TranslationR Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
|
From: Lincoln S. <ls...@cs...> - 2003-04-10 23:31:53
|
That's fine. I'll be interested in seeing how the translation works out. I've been translating using Bioperl's translate() method -- you can call it on a segment or on a feature(), and it will even handle splicing right if you've got the phase indicated. Lincoln On Tuesday 08 April 2003 05:13 pm, Charles Hauser wrote: > ALL, > > Preparing to load a chloroplast sequence & annotations into a new DB and > have a question about GFF formatting and the schema. > > On the last line shown I have gene product [name, id,codon_start, > transl_table, db_xref and translation] all listed as comments on one > line. > > Is this correct, or do I need to split each out onto separate lines? > > > Cp Chromosome Complete 1 203395 . + . Sequence Cp > Cp cgp repeat_region 1 203395 . - . transposon wendy ; note "putative > transposon" Cp cgp gene 2898 3851 . + . gene petA > Cp cgp CDS 2898 3851 . + . gene petA ; product "cytochrome f" ; > protein_id "DAA00904.1" ; codon_start 1 ; transl_table 11 ; db_xref > "GI:28269726" ; translation > MSNQVFTTLRAATLAVILGMAGGLAVSPAQAYPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTV >FEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPG >KKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSI >EKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPARIQGLLVFFSFVLLTQVLLVLK >KKQFEKVQLAEMNF > > > Charles > > > > ------------------------------------------------------- > This SF.net email is sponsored by: ValueWeb: > Dedicated Hosting for just $79/mo with 500 GB of bandwidth! > No other company gives more support or power for your dedicated server > http://click.atdmt.com/AFF/go/sdnxxaff00300020aff/direct/01/ > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- Lincoln Stein ls...@cs... Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) |
|
From: Marc L. <Mar...@de...> - 2003-04-10 22:01:32
|
Hi Charles,
There is a way using an aggregator:
aggregators = est{exon:est2genome}
[EST]
feature = est
connector = dashed
glyph = segments
bgcolor = limegreen
fgcolor = black
height = 4
stranded = 1
connector = solid
key = ESTs aligned by Exonerate
HTH,
Marc
> -----Original Message-----
> From: Charles Hauser [mailto:ch...@du...]
> Sent: Thursday, April 10, 2003 7:09 PM
> To: GBrowse
> Subject: [Gmod-gbrowse] GBrowse: connecting clone segments
>
>
> All,
>
>
> I am trying to connect segments of est clones where the clone spans an
> intron.
>
>
> I'd like to:
>
> - have the clone segments display on a single line
> - connect clone segments using 'connector'
> - do away with the "" surrounding clone id
>
> here's to code I'm currently using to generate the
> group info:
>
> ($clone =
> ($feat->each_tag_value('sequence'))[0]) =~ s/\"//g;
> $feat->add_tag_value('transcript', $clone);
>
>
>
> sample gff for a clone spaning an intron:
>
> scaffold_688 est2genome exon 4190 4351 1839
> - . Transcript "1031074A03.y1"
> scaffold_688 est2genome exon 4535 4656 1839
> - . Transcript "1031074A03.y1"
> scaffold_688 est2genome exon 4790 4902 1839
> - . Transcript "1031074A03.y1"
>
>
> current config file:
>
> [EST]
> feature = exon:est2genome
> feature_low = similarity:est2genome
> glyph = segments
> bgcolor = limegreen
> fgcolor = black
> height = 4
> stranded = 1
> connector = solid
> key = ESTs aligned by Exonerate
>
>
>
> Thanks,
>
> Chuck
>
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Etnus, makers of
> TotalView, The debugger
> for complex code. Debugging C/C++ programs can leave you
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>
|
|
From: Charles H. <ch...@du...> - 2003-04-10 17:10:00
|
All,
I am trying to connect segments of est clones where the clone spans an
intron.
I'd like to:
- have the clone segments display on a single line
- connect clone segments using 'connector'
- do away with the "" surrounding clone id
here's to code I'm currently using to generate the group info:
($clone = ($feat->each_tag_value('sequence'))[0]) =~ s/\"//g;
$feat->add_tag_value('transcript', $clone);
sample gff for a clone spaning an intron:
scaffold_688 est2genome exon 4190 4351 1839 - . Transcript "1031074A03.y1"
scaffold_688 est2genome exon 4535 4656 1839 - . Transcript "1031074A03.y1"
scaffold_688 est2genome exon 4790 4902 1839 - . Transcript "1031074A03.y1"
current config file:
[EST]
feature = exon:est2genome
feature_low = similarity:est2genome
glyph = segments
bgcolor = limegreen
fgcolor = black
height = 4
stranded = 1
connector = solid
key = ESTs aligned by Exonerate
Thanks,
Chuck
|
|
From: Charles H. <ch...@du...> - 2003-04-08 21:15:08
|
ALL, Preparing to load a chloroplast sequence & annotations into a new DB and have a question about GFF formatting and the schema. On the last line shown I have gene product [name, id,codon_start, transl_table, db_xref and translation] all listed as comments on one line. Is this correct, or do I need to split each out onto separate lines? Cp Chromosome Complete 1 203395 . + . Sequence Cp Cp cgp repeat_region 1 203395 . - . transposon wendy ; note "putative transposon" Cp cgp gene 2898 3851 . + . gene petA Cp cgp CDS 2898 3851 . + . gene petA ; product "cytochrome f" ; protein_id "DAA00904.1" ; codon_start 1 ; transl_table 11 ; db_xref "GI:28269726" ; translation MSNQVFTTLRAATLAVILGMAGGLAVSPAQAYPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPARIQGLLVFFSFVLLTQVLLVLKKKQFEKVQLAEMNF Charles |
|
From: Lincoln S. <ls...@cs...> - 2003-04-03 18:09:06
|
I'll try changing the request method to GET. There are some other proble= ms=20 with this, but maybe I can work around them. Lincoln On Tuesday 25 March 2003 06:44 pm, ko...@sf... wrote: > I don't suppose there's any way around that? We're trying to integrate > gbrowse into our main website which currently works best with IE. > > Korine > > On Tue, 25 Mar 2003 17:51:42 -0500 ls...@cs... wrote: > > > For example, if I search for a certain landmark or range, then clic= k > > > somewhere else on the genome overview, and then click somewhere els= e > > > > again > on the overview, I can't use the browser buttons to get back = to > > the > > > > previous view. > > > > That depends on what browser you're using. Netscape and Konqueror do = OK, > > but IE has problems (gives you a message about POST, right?) > > > > Lincoln > > > > -- > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > Lincoln D. Stein=09=09=09 Cold Spring Harbor Laboratory > > ls...@cs...=09=09=09=09 Cold Spring Harbor, NY > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > Korine Ung > Site Administrator/Laboratory Assistant > Brinkman Laboratory > Department of Molecular Biology and Biochemistry > Simon Fraser University > Tel: 604-291-5414 > Email: ko...@sf... --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
|
From: Scott C. <ca...@cs...> - 2003-04-03 14:44:50
|
On Thu, 2003-04-03 at 09:08, Lincoln Stein wrote: > ...lots of gbrowse news... > > and Bio::DB::GFF on PostGreSQL is still > a ways off. Actually, I just committed a Postgres adaptor to bioperl at Bio/DB/GFF/Adaptor/dbi/pg.pm which seems to work just fine. I've only tested it with the yeast database so far though. Hopefully the performance won't be too bad with a big data set. Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |
|
From: Lincoln S. <ls...@cs...> - 2003-04-02 16:27:29
|
Hi Foo, There is actually an in-memory version of the Bio::DB::GFF adaptor that r= uns=20 directly off flat files. However, it needs a tiny bit of work to make it= =20 compatible with gbrowse. Now that you've requested it, I've got the last= bit=20 of motivation needed to make it work. Lincoln On Thursday 27 March 2003 09:20 pm, Cheung, Foo wrote: > Hi All > > I was wondering whether you will be releasing a browser version that ru= ns > of flatfiles eg GFF or any other flatfile format Or if you could advise= me > the code to modify and I can hack at it. > > The browser is very cool and I was hoping to give your browser a spin w= ith > some new genome sequences we have! > > > many thanks in advance > kind regards > Foo > ;o) > > > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: > The Definitive IT and Networking Event. Be There! > NetWorld+Interop Las Vegas 2003 -- Register today! > http://ads.sourceforge.net/cgi-bin/redirect.pl?keyn0001en > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
|
From: Lincoln S. <ls...@cs...> - 2003-04-02 16:26:03
|
Hi Charles, Scott told me that you might be trying to load data located on one machin= e=20 onto a mysql server that is located on another machine. The ability to d= o=20 this depends on what version of mysql you are using as well as the=20 compile-time options and a complex series of configuration and permission= s=20 options. It's best to use the simple load_gff.pl script if you're in thi= s=20 situation. Lincoln On Monday 31 March 2003 04:16 pm, Scott Cain wrote: > Because load_gff.pl uses insert statements via DBI and doesn't depend o= n > MySQL's ability to load into tables from a file. > > On Mon, 2003-03-31 at 16:08, Charles Hauser wrote: > > > The other option is to use load_gff.pl instead of bulk_load_gff.pl. > > > load_gff.pl uses inserts to load the data, so it will be slower, bu= t is > > > much more likely to work. > > > > hummmmmmmmmmm, > > why should load_gff work and not bulk_load_gff???????? > > > > [chauser@gulliver Generic-Genome-Browser-1.50]$ perl load_gff.pl -d y= east > > --user chauser --pass xxx sample_data/yeast_data.gff > > sample_data/yeast_data.gff: loading... > > sample_data/yeast_data.gff: 13298 records loaded --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
|
From: Lincoln S. <ls...@cs...> - 2003-04-02 16:23:54
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Hi Michael, You should stick with a single coordinate system. Mixing chromosome=20 coordinates with clone coordinates is going to cause many confusing probl= ems=20 because the GFF database that underlies gbrowse wasn't set up by handle=20 relative coordinate systems. I would suggest something like this: I chromosome component 1 73202 . + . Target Clone:01b23 1 73202 I BLASTN similarity 10 1000 900 + . Target Hit:test 10 1000 That is, remove the explicit entries for the assembly clones (they are=20 implicit in the "component" line), and transform the BLASTN hits into=20 absolute coordinates relative to chromosome I. Lincoln On Wednesday 02 April 2003 06:45 am, Michael Thon wrote: > I am trying to load assembly information into a database for gbrowse. I > would like to use clones as reference sequences for features and load > assembly information so that the chromosome, represented by many clones= , > is displayed in the browser. the last 2 lines of GFF code shown below, > work fine when loaded into the database. When I include line 1 the > gbrowse pages fail to load. None of the example gff files included with > gbrowse seem to have assembly information. Does anyone have an example > gff file that includes the use of assembly information? > Thanks > Mike > > I chromosome component 1 73202 . + . Target Sequence:01b23 1 73202 > 01b23 assembly clone 1 73202 . + . Sequence "01b23" > 01b23 BLASTN similarity 10 1000 900 + . Target Sequence:test 10 1000 > > > > ------------------------------------------------------- > This SF.net email is sponsored by: ValueWeb: > Dedicated Hosting for just $79/mo with 500 GB of bandwidth! > No other company gives more support or power for your dedicated server > http://click.atdmt.com/AFF/go/sdnxxaff00300020aff/direct/01/ > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Lincoln D. Stein Cold Spring Harbor Laboratory ls...@cs...=09=09=09 Cold Spring Harbor, NY =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D |
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From: Michael T. <mr...@un...> - 2003-04-02 11:45:27
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I am trying to load assembly information into a database for gbrowse. I would like to use clones as reference sequences for features and load assembly information so that the chromosome, represented by many clones, is displayed in the browser. the last 2 lines of GFF code shown below, work fine when loaded into the database. When I include line 1 the gbrowse pages fail to load. None of the example gff files included with gbrowse seem to have assembly information. Does anyone have an example gff file that includes the use of assembly information? Thanks Mike I chromosome component 1 73202 . + . Target Sequence:01b23 1 73202 01b23 assembly clone 1 73202 . + . Sequence "01b23" 01b23 BLASTN similarity 10 1000 900 + . Target Sequence:test 10 1000 |
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