mummer-help — For general MUMmer questions and help.

[MUMmer-help] how to deal with the file .coords resulted from program

[Marwa E. <dr....@ho...>]

 hello, 


My 2  Question are 


1) how to deal with the file .coords  resulted from program rather than show it in mapview and dot plot??''i mean how can to extract the net results from this file ??

2) what i am understood from this file that the  program compare all Quires with the one reference , but my study aim is to make the alignment of interested 

gene in all Queries and reference to each other '' i mean compare all  Queries to each other and with the reference also, but not only compare each Query  to 

reference   , so is this option can  be occurred or even can understand that from file .coords "????

thanks u 
  		 	   		  

[MUMmer-help] how to deal with the File .coords resulted from the program??

[Marwa E. <dr....@ho...>]

Hello every Body, 


My  2 Questions are


1) how to deal with the File .coords resulted from the program rather than show the mapview or dotplot?? i mean how can i extract the net results from this file ???


2)what i understood from file . coords that :the program compare all the Quires to reference , but my aim is to make the alignment of interested gene  in all 

Quires and  reference, '' i mean compare all the Quires & reference to each other but not compare each Query to reference only but also compare the Quires to 

each other '' so this option can be occurred or even can i understand this from file.coords??? 

thank u
 		 	   		  

Re: [MUMmer-help] help with mummerplot

[Adam P. <aph...@gm...>]

The newer versions of gnuplot changed to a different tic scale syntax.
Either upgrade to a newer version of gnuplot that supports this new format,
e.g. gnuplot 4.4 or higher, or you can edit the mummerplot perl code to
remove this offending command.

Best,
-Adam


On Tue, Sep 4, 2012 at 1:33 PM, ramakrishna sompallae <
ram...@gm...> wrote:

> Hi,
>
> I am using Mummer for the first time. It seems to be a great program for
> sequence analysis. I am trying to align my contigs from a denovo assembly
> to refernece genome to get an idea about how good is the sequence
> covereage. when I use the mummerplot it is showing the following error.
>
> gnuplot> set tics scale 0
>
>             "temp.gp", line 7: ';' expected
>
> WArning: Unable to run 'gnuplot temp.gp', Inappropraite ioctl for device
>
> I looked through the help files and followed all the instructions but
> nothing worked. I will be grateful if you can help me to fix this issue.
>
> thanks for reading and looking forward for your reply.
>
> Regards
> Rama
>
> On Tue, Sep 4, 2012 at 12:28 PM, ramakrishna sompallae <
> ram...@ui...> wrote:
>
>> Hi,
>>
>> I am using Mummer for the first time. It seems to be a great program for
>> sequence analysis. I am trying to align my contigs from a denovo assembly
>> to refernece genome to get an idea about how good is the sequence
>> covereage. when I use the mummerplot it is showing the following error.
>>
>> gnuplot> set tics scale 0
>>
>>             "temp.gp", line 7: ';' expected
>>
>> WArning: Unable to run 'gnuplot temp.gp', Inappropraite ioctl for device
>>
>> I looked through the help files and followed all the instructions but
>> nothing worked. I will be grateful if you can help me to fix this issue.
>>
>> thanks for reading and looking forward for your reply.
>>
>> Regards
>> Rama
>>
>>
>>
>> --
>> Ramakrishna Sompallae
>> Bioinformatics Core Facility
>> University of Iowa
>> 113A EMRB
>> Iowa City, IA 52242
>> http://bioinform-div.healthcare.uiowa.edu/
>>
>>
>>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

Re: [MUMmer-help] can i use mummer for interested gene but not whole genomes‏

[Adam P. <aph...@gm...>]

Simply make a fasta file including only your gene of interest. The program
is not limited to whole-genomes, and it will align any fasta input.

-Adam

On Sat, Sep 1, 2012 at 11:28 AM, Marwa Essam <dr....@ho...> wrote:

>  Hello,
>
> i study certain gene in several types E.coli , i would like to make the
> alignment of this gene only , but what i understood from MUMmer program
> ''promer
>
> option'' that it deal with whole genomes and the resulted figure again
> represented the whole genomes ....that is mean the using of whole genome is
> obligatory .
>
> is it right ??? but i wanna make the alignment of my interested gene and
> represented it only not whole genomes in figure as dot plot or map-view so
> is there is
>
> any way to apply this by MUMmer program???
>
>
>
> Really i get frustrated because i interest with this amazing program. I'm
> sorry for Occupying your time , you are very kind to give me so much help
> in answering my  asking
>
>
> thanks
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

Re: [MUMmer-help] Help With show-coords

[Adam P. <aph...@gm...>]

Hi Owain,
That's very odd and I have no explanation for that. The LEN column is
simply computed as E1-S1 in the code, so it should always match up. Can you
send me your .delta file so I can take a look?

Thanks,
-Adam


On Thu, Aug 30, 2012 at 6:57 PM, <OM...@tg...> wrote:

> Hello,
>
> My name is Owain Moss, and I work at TGen North - Division for Pathogen
> Genomics under Lance Price. I am currently writing a script that requires a
> comparison of a reference genome and a query genome. We want to take the
> coordinates in the reference sequence that were matched to by the query
> sequence, and use them to perform an analysis. We are using the ouput from
> show-coords to get these coordinates; however, we are having trouble
> interpreting it. I have attached the exact file we are using as a
> reference, so please refer to that as I continue my explanation.
>
> The main issue is that the lengths of some of the reference regions ( [len
> 1] ) don't match up with the calculated lengths of the corresponding
> alignment regions. For example, in the first line of the table ( [len 1] =
> 24374 ) doesn't match up with the  range of coordinates ( [E1] - [S1] + 1 =
> (12251 -1 + 1 = 12251) ). Can you explain what's going on here? I looked a
> the MUMmer documentation, but I couldn't find an explanation.
>
> Thanks,
> Owain Moss
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

Re: [MUMmer-help] help with mummerplot

[ramakrishna s. <ram...@gm...>]

Hi,

I am using Mummer for the first time. It seems to be a great program for
sequence analysis. I am trying to align my contigs from a denovo assembly
to refernece genome to get an idea about how good is the sequence
covereage. when I use the mummerplot it is showing the following error.

gnuplot> set tics scale 0

            "temp.gp", line 7: ';' expected

WArning: Unable to run 'gnuplot temp.gp', Inappropraite ioctl for device

I looked through the help files and followed all the instructions but
nothing worked. I will be grateful if you can help me to fix this issue.

thanks for reading and looking forward for your reply.

Regards
Rama

On Tue, Sep 4, 2012 at 12:28 PM, ramakrishna sompallae <
ram...@ui...> wrote:

> Hi,
>
> I am using Mummer for the first time. It seems to be a great program for
> sequence analysis. I am trying to align my contigs from a denovo assembly
> to refernece genome to get an idea about how good is the sequence
> covereage. when I use the mummerplot it is showing the following error.
>
> gnuplot> set tics scale 0
>
>             "temp.gp", line 7: ';' expected
>
> WArning: Unable to run 'gnuplot temp.gp', Inappropraite ioctl for device
>
> I looked through the help files and followed all the instructions but
> nothing worked. I will be grateful if you can help me to fix this issue.
>
> thanks for reading and looking forward for your reply.
>
> Regards
> Rama
>
>
>
> --
> Ramakrishna Sompallae
> Bioinformatics Core Facility
> University of Iowa
> 113A EMRB
> Iowa City, IA 52242
> http://bioinform-div.healthcare.uiowa.edu/
>
>
>

[MUMmer-help] can i use mummer for interested gene but not whole genomes‏

[Marwa E. <dr....@ho...>]

Hello, 
 
i study certain gene in several types E.coli , i would 
like to        make the alignment of this gene only , but what i 
understood        from MUMmer program ''promer 

        option'' 
that it deal with whole genomes and the resulted figure        again 
represented the whole genomes ....that is mean the using        of whole
 genome is obligatory . 

        is it right ??? but i wanna make
 the alignment of my interested        gene and represented it only not 
whole genomes in figure as dot        plot or map-view  so is there is 

        any way to apply this by MUMmer program??? 


    

        Really i get frustrated because i interest with this amazing        program. I'm sorry for Occupying          your time , you             are very kind to give me so much help in answering my  asking 


thanks
 		 	   		  

[MUMmer-help] Help With show-coords

[<OM...@tg...>]

Hello,

My name is Owain Moss, and I work at TGen North - Division for Pathogen Genomics under Lance Price. I am currently writing a script that requires a comparison of a reference genome and a query genome. We want to take the coordinates in the reference sequence that were matched to by the query sequence, and use them to perform an analysis. We are using the ouput from show-coords to get these coordinates; however, we are having trouble interpreting it. I have attached the exact file we are using as a reference, so please refer to that as I continue my explanation.

The main issue is that the lengths of some of the reference regions ( [len 1] ) don't match up with the calculated lengths of the corresponding alignment regions. For example, in the first line of the table ( [len 1] = 24374 ) doesn't match up with the   range of coordinates ( [E1] - [S1] + 1 = (12251 -1 + 1 = 12251) ). Can you explain what's going on here? I looked a the MUMmer documentation, but I couldn't find an explanation.

Thanks,
Owain Moss

[MUMmer-help] Help With show-coords

[<OM...@tg...>]

Hello,

My name is Owain Moss, and I work at TGen North - Division for Pathogen Genomics under Lance Price. I am currently writing a script that requires a comparison of a reference genome and a query genome. We want to take the coordinates in the reference sequence that were matched to by the query sequence, and use them to perform an analysis. We are using the ouput from show-coords to get these coordinates; however, we are having trouble interpreting it. I have attached the exact file we are using as a reference, so please refer to that as I continue my explanation.

The main issue is that the lengths of some of the reference regions ( [len 1] ) don't match up with the calculated lengths of the corresponding alignment regions. For example, in the first line of the table ( [len 1] = 24374 ) doesn't match up with the  range of coordinates ( [E1] - [S1] + 1 = (12251 -1 + 1 = 12251) ). Can you explain what's going on here? I looked a the MUMmer documentation, but I couldn't find an explanation.

Thanks,
Owain Moss

[MUMmer-help] Help with show-coords

[<OM...@tg...>]

Hello,

My name is Owain Moss, and I work at TGen North - Division for Pathogen Genomics under Lance Price. I am currently writing a script that requires a comparison of a reference genome and a query genome. We want to take the coordinates in the reference sequence that were matched to by the query sequence, and use them to perform an analysis. We are using the ouput from show-coords to get these coordinates; however, we are having trouble interpreting it. I have attached the exact file we are using as a reference, so please refer to that as I continue my explanation.

The main issue is that the lengths of some of the reference regions ( [len 1] ) don't match up with the calculated lengths of the corresponding alignment regions. For example, in the first line of the table ( [len 1] = 24374 ) doesn't match up with the range of coordinates ( [E1] - [S1] + 1 = (12251 -1 + 1 = 12251) ). Can you explain what's going on here? I looked a the MUMmer documentation, but I couldn't find an explanation.

Thanks,
Owain Moss

[MUMmer-help] new user on problem of mapview

[Jiuhai Z. <zha...@ho...>]

Hi,I have some problems as follows when i run mapview using examples by " mapview -n 1 -p mapview promer.coords D_melanogaster_2Rslice.utr D_melanogaster_2Rslice.cds" (http://mummer.sourceforge.net/examples/#mapview) . I check the seq ID, I cannot find any difference. Can you help me figure out what is the problem? Thanks. jiuhai  ERROR in the input files ! The reference seq ID can't be found in GFF files !      The first column in the GFF file should be the ID of the reference seq.       The alignments file should provide the same info in the column before the last one.            Here are some example records for the GFF file:           gnl|FlyBase|X Dmel3 initial-exon 2155 2413 . - . X_CG3038.1      gnl|FlyBase|X Dmel3 last-exon 1182 2077 . - . X_CG3038.1      ...      The fields are :      <seq_ID> <source> <exon type> <start> <end> <score> <strand> <frame> <gene_name> 		 	   		  

[MUMmer-help] QUE

[Saeid M. <mal...@gm...>]

Dear madam/sir,



My name is Saeid Malek Zadeh and I am working in Pasteur institute. First
as you mentioned I subscribed on the site and now I am a subscribed
member. our project is comparing of whole proteome and genome of
two organisms. our two organisms are fungous. We want compare whole
proteome and genome of these organisms and find hit and no-hit proteins and
genes. please help me.



best regards,



Saeid Malek Zadeh,

[MUMmer-help] Regarding mummer's -maxmatch

[Gurusaran M. <sat...@gm...>]

Dear Colleagues

I have been using mummer lately and I found it to be amazing. But while
using mummer I came across -maxmatch and I learned that -mumreference is
the default program option.

What exactly does -maxreference mean? How exactly does -maxreference and
-maxmatch differ? I went through the manual but I couldn't get a hold of it.

As I am from biology background and not from computer science, please help
me understand this using layman's term.

I would be grateful if I am helped in this regard.

Eagerly awaiting for a reply.

Warm regards,

Gurusaran M,
Research Assistant,
Supercomputer Education and Research Centre,
Indian Institute of Science,
Bangalore,
India.

Re: [MUMmer-help] Gapless alignments with MUMmer?

[Dan B. <dan...@gm...>]

Many thanks for the clear description Adam, that explains why it was
taking so long with --maxgap=0!

I'll let you know how the tests go.


Cheers
Dan.

On 19 July 2012 20:37, Adam Phillippy <aph...@gm...> wrote:
> Whoops, that would be
>
>> nucmer --banded -D 0 (other parameters here...)
>
>
> On Thu, Jul 19, 2012 at 3:36 PM, Adam Phillippy <aph...@gm...>
> wrote:
>>
>> Hi Dan,
>> I assume by "gapless" you mean no insertions/deletions in the alignment?
>> The nucmer terminology isn't consistent with this definition. Maxgap only
>> defines the match clustering behavior, not the extension and gapped
>> alignment behavior. And in this context, gap doesn't mean indel, it just
>> means the non-identical space between to exact matches. By setting it to
>> zero, none of the matches were being clustered and nucmer tried to extend
>> alignments from all the matches individually, which would take much longer
>> than its usual behavior of trying to extend only to the next match in a
>> cluster (the alignment extension is faster if it knows where it's going
>> beforehand).
>>
>> Nucmer doesn't have a natural gapless extension mode. However, there's a
>> newly added option in nucmer, -D, that controls the alignment "banding"
>> behavior. This can be used to control the largest indel inserted in an
>> alignment, but I haven't tested it for a value of "zero" and I'm not
>> confident it will work, but if you're going to try something, try that! :)
>> You also will need to turn on the strict banding behavior with --banded.
>>
>> > nucmer --banded -D (your other parameters here ...)
>>
>> Best,
>> -Adam
>>
>>
>> On Fri, Jul 13, 2012 at 6:59 PM, Dan Bolser <dan...@gm...> wrote:
>>>
>>> Hello,
>>>
>>> How can I configure MUMmer to produce gapless alignments? I tried
>>> setting --maxgap (nucmer) to zero, but weirdly this caused the
>>> algorithm to run about 100 times slower, and the output still
>>> contained large (>20) gaps in the reference.
>>>
>>> I would have thought disallowing gaps would speed up the alignment...
>>> anyway, I must be doing something wrong, as the output still contains
>>> gaps.
>>>
>>>
>>> Cheers,
>>> Dan.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond. Discussions
>>> will include endpoint security, mobile security and the latest in malware
>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>> _______________________________________________
>>> MUMmer-help mailing list
>>> MUM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>
>>
>

Re: [MUMmer-help] question about show-snps

[Adam P. <aph...@gm...>]

Hi Jin,
show-snps reports any difference contained within an aligned block,
reporting one base per line. A multi-base insert in this format will be
reported as a number of single-base indels, all with the same coordinate in
the reference (or query depending if it is an insertion or deletion).

To capture large insertions or deletions requires parsing the output of
show-coords. Show-coords reports the positions of the aligned blocks, so
any indel too big to be contained in an alignment will exist as an
unaligned region between two aligned blocks. You can sort the output of
show-coords to help identifying these regions.

To determine how large an indel is tolerated in an aligned block you can set

> nucmer --banded -D x

and set 'x' to be the size of the largest indel you would like to be
contained in an alignment, and thus reported at the base level in show-snps.

Best,
-Adam


On Thu, Jul 12, 2012 at 1:52 AM, Yiching Tang <jin...@gm...> wrote:

> hi there:
> just an unexpected observation when I use show-snps which is that all
> insertion/deletion are single-base variants.
> is it something that I should see in nucmer.snps file? Or, is there any
> parameters I should employee/ you would suggest when using  show-snps
> scripts?
> thanks in advance!
>
> Sincere,
> Jin
>
> --
> Best Regards,
> Yiching Tang
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

Re: [MUMmer-help] Gapless alignments with MUMmer?

[Adam P. <aph...@gm...>]

Whoops, that would be

> nucmer --banded -D 0 (other parameters here...)

On Thu, Jul 19, 2012 at 3:36 PM, Adam Phillippy <aph...@gm...>wrote:

> Hi Dan,
> I assume by "gapless" you mean no insertions/deletions in the alignment?
> The nucmer terminology isn't consistent with this definition. Maxgap only
> defines the match clustering behavior, not the extension and gapped
> alignment behavior. And in this context, gap doesn't mean indel, it just
> means the non-identical space between to exact matches. By setting it to
> zero, none of the matches were being clustered and nucmer tried to extend
> alignments from all the matches individually, which would take much longer
> than its usual behavior of trying to extend only to the next match in a
> cluster (the alignment extension is faster if it knows where it's going
> beforehand).
>
> Nucmer doesn't have a natural gapless extension mode. However, there's a
> newly added option in nucmer, -D, that controls the alignment "banding"
> behavior. This can be used to control the largest indel inserted in an
> alignment, but I haven't tested it for a value of "zero" and I'm not
> confident it will work, but if you're going to try something, try that! :)
> You also will need to turn on the strict banding behavior with --banded.
>
> > nucmer --banded -D (your other parameters here ...)
>
> Best,
> -Adam
>
>
> On Fri, Jul 13, 2012 at 6:59 PM, Dan Bolser <dan...@gm...> wrote:
>
>> Hello,
>>
>> How can I configure MUMmer to produce gapless alignments? I tried
>> setting --maxgap (nucmer) to zero, but weirdly this caused the
>> algorithm to run about 100 times slower, and the output still
>> contained large (>20) gaps in the reference.
>>
>> I would have thought disallowing gaps would speed up the alignment...
>> anyway, I must be doing something wrong, as the output still contains
>> gaps.
>>
>>
>> Cheers,
>> Dan.
>>
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> MUMmer-help mailing list
>> MUM...@li...
>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>
>
>

Re: [MUMmer-help] Gapless alignments with MUMmer?

[Adam P. <aph...@gm...>]

Hi Dan,
I assume by "gapless" you mean no insertions/deletions in the alignment?
The nucmer terminology isn't consistent with this definition. Maxgap only
defines the match clustering behavior, not the extension and gapped
alignment behavior. And in this context, gap doesn't mean indel, it just
means the non-identical space between to exact matches. By setting it to
zero, none of the matches were being clustered and nucmer tried to extend
alignments from all the matches individually, which would take much longer
than its usual behavior of trying to extend only to the next match in a
cluster (the alignment extension is faster if it knows where it's going
beforehand).

Nucmer doesn't have a natural gapless extension mode. However, there's a
newly added option in nucmer, -D, that controls the alignment "banding"
behavior. This can be used to control the largest indel inserted in an
alignment, but I haven't tested it for a value of "zero" and I'm not
confident it will work, but if you're going to try something, try that! :)
You also will need to turn on the strict banding behavior with --banded.

> nucmer --banded -D (your other parameters here ...)

Best,
-Adam


On Fri, Jul 13, 2012 at 6:59 PM, Dan Bolser <dan...@gm...> wrote:

> Hello,
>
> How can I configure MUMmer to produce gapless alignments? I tried
> setting --maxgap (nucmer) to zero, but weirdly this caused the
> algorithm to run about 100 times slower, and the output still
> contained large (>20) gaps in the reference.
>
> I would have thought disallowing gaps would speed up the alignment...
> anyway, I must be doing something wrong, as the output still contains
> gaps.
>
>
> Cheers,
> Dan.
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>

[MUMmer-help] Gapless alignments with MUMmer?

[Dan B. <dan...@gm...>]

Hello,

How can I configure MUMmer to produce gapless alignments? I tried
setting --maxgap (nucmer) to zero, but weirdly this caused the
algorithm to run about 100 times slower, and the output still
contained large (>20) gaps in the reference.

I would have thought disallowing gaps would speed up the alignment...
anyway, I must be doing something wrong, as the output still contains
gaps.


Cheers,
Dan.

[MUMmer-help] question about show-snps

[Yiching T. <jin...@gm...>]

hi there:
just an unexpected observation when I use show-snps which is that all
insertion/deletion are single-base variants.
is it something that I should see in nucmer.snps file? Or, is there any
parameters I should employee/ you would suggest when using  show-snps
scripts?
thanks in advance!

Sincere,
Jin

-- 
Best Regards,
Yiching Tang

[MUMmer-help] (no subject)

[Ahmad N. <ahm...@ym...>]

http://wadebowen.com/scripts/rssbox/cache/ofnwp.html?kju=exo.jxveza&jtgi=laz.zaif&lva=xuzs

[MUMmer-help] Spam Confirmation

[Ahmad N. <ahm...@ym...>]

Dear All

On last three days ago my email was hack, than if you was received hyperlink from this email.
I would tell you that the link is a spam so just ignore it.
Now my email address has been fixed.
I hope we still on touch with this email address.

Best Regards
Ahmad Najib 
Head of Pharmacognosy-Phytochemistry Lab.
Faculty of Pharmacy 
Moslem University of Indonesia

[MUMmer-help] (no subject)

[Ahmad N. <ahm...@ym...>]

http://www.amynparker.com/wp-content/themes/vigilance/nsdotws.html?nqq=nl.nck&bbcin=kjnk.kk&kkyj=ufpn

Re: [MUMmer-help] Mummer Tigr::Foundation problem

[Adam P. <aph...@gm...>]

Hi Henri,
Can you send me the mummerplot script you are attempting to execute? Also,
what version of perl and what distro of linux are you running?

Thanks,
-Adam


On Wed, May 16, 2012 at 11:59 AM, Henri <he...@tf...> wrote:

> Hi,
>
> I'm having problem running mummer plot. The problem report is following:
>
> defined(%hash) is deprecated at ./mummerplot line 884.
>        (Maybe you should just omit the defined()?)
> defined(%hash) is deprecated at ./mummerplot line 894.
>        (Maybe you should just omit the defined()?)
> defined(%hash) is deprecated at ./mummerplot line 981.
>        (Maybe you should just omit the defined()?)
> defined(%hash) is deprecated at ./mummerplot line 991.
>        (Maybe you should just omit the defined()?)
> defined(%hash) is deprecated at ./mummerplot line 1034.
>        (Maybe you should just omit the defined()?)
> defined(%hash) is deprecated at ./mummerplot line 1044.
>        (Maybe you should just omit the defined()?)
> Can't locate object method "new" via package "TIGR::Foundation" (perhaps
> you forgot to load "TIGR::Foundation"?) at ./mummerplot line 186.
>
>
> I've seen same problem in source forge message boards but haven't
> encountered any solutions.
>
>
>
> Best regards,
> H
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>

[MUMmer-help] Mummer Tigr::Foundation problem

[Henri <he...@tf...>]

Hi,

I'm having problem running mummer plot. The problem report is following:

defined(%hash) is deprecated at ./mummerplot line 884.
	(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at ./mummerplot line 894.
	(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at ./mummerplot line 981.
	(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at ./mummerplot line 991.
	(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at ./mummerplot line 1034.
	(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at ./mummerplot line 1044.
	(Maybe you should just omit the defined()?)
Can't locate object method "new" via package "TIGR::Foundation" (perhaps you forgot to load "TIGR::Foundation"?) at ./mummerplot line 186.


I've seen same problem in source forge message boards but haven't encountered any solutions.



Best regards,
H

Re: [MUMmer-help] Nucmer p-value

[Adam P. <aph...@gm...>]

Hi Nagarjun,
Sorry, there is no code in the current version of MUMmer that does this.
You will have to score the alignments yourself if you require a p-value.

-Adam


On Sat, Apr 28, 2012 at 1:36 AM, Nagarjun V <arj...@gm...> wrote:

> Hi,
>
> Could you please let me know if its possible to calculate a p-value for
> the alignments reported by Nucmer?
>
> My understanding is that sensitivity is determined by "Minimum cluster
> length (default 65)" and "Minimum length of an maximal exact match
> (default 20)". However, the probability of match will depend on the
> size(greater the size greater the chance of hits longer than 20) of the
> reference and query sequence files and similarity(more similar the
> sequences greater the chance of clusters longer than 65) between sequences.
>
> Nagarjun
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>