[maker-devel] ipr_update_gff

Wed Nov 18 21:39:20 MST 2009

Hi Shane and Barry,

Generally, anything that goes into Chado via GFF can come out via a
callback to be used in a gbrowse conf file, although I'm not positive
that Dbxref accessions are readily available, but if not, the adaptor
can be modified to make it easy.

Scott

On Wed, Nov 18, 2009 at 11:27 PM, Barry Moore
<barry.moore at genetics.utah.edu> wrote:
> Shane,
>
> Nope, we're just parsing tab delimited text files from IPRScan.  Actually I
> have to confess, I don't think I've ever run IPRScan myself, Carson has
> handled that on all our projects thus far, so I didn't know that IPRScan did
> an XML format.  Anyway, it's capturing ID for matches to these databases:
>
> ProDom
> PRINTS
> Gene3D
> PANTHER
> Pfam
> PIR
> SMART
> JCVI_TIGRFAMS
> Prosite
> GO
>
> And ignoring results from:
>
> Seg
> Coil
> SignalPHMM
>
> The GO terms go as Ontology_term attributes and eveything else as a Dbxref.
>
> I'm not the best person to ask about GBrowse/Chaod configuration.  I spoke
> with John Hamilton of the Pythium project some time ago and I seem to recall
> that they used callbacks in the conf file that would put additional data
> into popup ballon with the features but I'm not sure where they were
> stashing the details in Chado.  His address is hamilton at plantbiology dot
> msu dot edu and I'm sure he'd be happy to offer suggestions on how they've
> done this.
>
> B
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
> On Nov 18, 2009, at 5:02 PM, Shane Brubaker wrote:
>
>> Hi Barry, I had a couple more questions about ipr_update_gff.  Does it
>> expect the standard XML-style output from iprscan?  When I run it I get some
>> uninitialized value messages.
>>
>> Also, does it just update the dbxref or would it transfer all the
>> information, for example the domains found on the protein/gene?
>>
>> In general is there a place I could put a bunch of additional information
>> about a gene and have it show up in Gbrowse (in the description line
>> perhaps?)
>>
>> Thanks.
>>
>>
>>
>>
>>
>>
>>
>> -----Original Message-----
>> From: Barry Moore [mailto:barry.moore at genetics.utah.edu]
>> Sent: Wednesday, November 18, 2009 3:00 PM
>> To: Shane Brubaker
>> Cc: maker-devel at yandell-lab.org
>> Subject: Re: [maker-devel] maker-devel Digest, Vol 18, Issue 4
>>
>> Hi Shane,
>>
>> Yeah, I put on my TODO list after your first mail to fix those scripts
>> so they use BioPerl's SearchIO class so that any blast will be
>> supported.  The scripts are parsing the fasta files to get the
>> detailed header information (since this doesn't show up in the tabular
>> blast output, so we could also allow some pass in code reference that
>> would parse nr/np or whatever fasta header.  Finally we could do the
>> output as a configurable printf so that users could define the output
>> on the fly.  Those are definitely improvements to the script that I'm
>> happy to do since it will benefit us and the MAKER community in
>> general.  I'm in the midst of trying to get a paper out the door, so
>> I'm looking at a week or two turn around time on that I'd say, so if
>> you know perl and need it sooner, I'm happy to accept a patch as well.
>>
>> B
>>
>> Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>>
>>
>>
>>
>> On Nov 18, 2009, at 3:48 PM, Shane Brubaker wrote:
>>
>>> Hi Barry, I would like to use maker_functional_gff, but I noticed it
>>> refers to Wu-Blast.
>>>      I would like to use it with NCBI blast (I couldn't afford Wu-
>>> Blast!), do you know if that could work, and what would be the
>>> equivalent of -m 2 format?
>>>      I would also kind of like to try this with a blast vs. nr in
>>> addition to using Swissprot, do you think that would be possible?
>>>
>>>      On a related note, is there a field(s) I can put things into
>>> in Chado that will show up in Gbrowse, such that I could just write
>>> my own custom scripts which transfer annotations to enhance my Maker-
>>> annotated genome?
>>>
>>>
>>> Thanks much.
>>>
>>>
>>> -----Original Message-----
>>> From: maker-devel-bounces at yandell-lab.org [mailto:maker-devel-
>>> bounces at yandell-lab.org] On Behalf Of maker-devel-request at yandell-lab.org
>>> Sent: Monday, November 16, 2009 3:49 PM
>>> To: maker-devel at yandell-lab.org
>>> Subject: maker-devel Digest, Vol 18, Issue 4
>>>
>>> Send maker-devel mailing list submissions to
>>>      maker-devel at yandell-lab.org
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>>>
>>>
>>> Today's Topics:
>>>
>>>  1. Question on ESTs and functional annotations (Shane Brubaker)
>>>  2. Re: Question on ESTs and functional annotations (Barry Moore)
>>>  3. Re: Question on ESTs and functional annotations (Shane Brubaker)
>>>  4. Re: Question on ESTs and functional annotations (Carson Holt)
>>>  5. Re: Question on ESTs and functional annotations (Shane Brubaker)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Mon, 16 Nov 2009 12:45:29 -0800
>>> From: Shane Brubaker <SBrubaker at Aurorabiofuels.com>
>>> Subject: [maker-devel] Question on ESTs and functional annotations
>>> To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>>> Message-ID:
>>>      <4F28B35C91C1B040B7183D28726A8663264CEF1524 at Exchange.aurora.local
>>>>
>>> Content-Type: text/plain; charset="us-ascii"
>>>
>>> Hi, I had a couple of general questions.
>>>
>>> 1.  What are the EST blastn results that are found in the MAKER gff3
>>> output?  I thought these might be a track of my ESTs mapped onto the
>>> genome, but they seem to contain pieces of the EST but not the
>>> entire thing?
>>> 2.  What is a good way to add functional annotation to the gene
>>> results? I have a track of protein matches, I used Swissprot as my
>>> set of proteins.  So I can see proteins and I can look up my
>>> Swissprot accession number and find out more about that gene.  But
>>> what I really want is to click on my actual gene models (from
>>> augustus or snap) and then have some functional annotation on that
>>> page which has been transferred onto the gene, as well as some links
>>> out to the appropriate external sites.  Is there a good general
>>> approach for doing that?
>>>
>>>
>>> Thanks,
>>> Shane
>>>
>>> This email and any attachments thereto may contain private,
>>> confidential, and privileged material for the sole use of the
>>> intended recipient.  Any review, copying, or distribution of this
>>> email (or any attachments thereto) by others is strictly
>>> prohibited.  If you are not the intended recipient, please contact
>>> the sender immediately and permanently delete the original and any
>>> copies of this email and any attachments thereto.
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 2
>>> Date: Mon, 16 Nov 2009 15:35:25 -0700
>>> From: Barry Moore <barry.moore at genetics.utah.edu>
>>> Subject: Re: [maker-devel] Question on ESTs and functional annotations
>>> To: Shane Brubaker <SBrubaker at Aurorabiofuels.com>
>>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>>> Message-ID: <6D22E2BC-73A1-4570-BA2F-307B15EFD434 at genetics.utah.edu>
>>> Content-Type: text/plain; charset="us-ascii"; format=flowed; delsp=yes
>>>
>>> Shane,
>>>
>>> With regards to your second question...we've got a few scripts in the
>>> bin directory that we have used to add functional annotations to MAKER
>>> output.  They are:
>>>
>>> maker_functional_fasta
>>> maker_functional_gff
>>> ipr_update_gff
>>>
>>> The first two will take a blastp output from your MAKER proteins
>>> against swissprot and add this sort of thing:
>>>
>>> name:"Serine-aspartate repeat-containing protein I (Staphylococcus
>>> saprophyticus)"
>>> Note="Serine-aspartate repeat-containing protein I (Staphylococcus
>>> saprophyticus)"
>>>
>>> to your fasta and GFF files respectively.  It's not currently adding
>>> the swissprot ID to that output, but it would be trivial to alter
>>> either or both to do so.
>>>
>>> Also a great (but CPU costly) way to get deeper functional annotations
>>> is to run IPRscan on your MAKER proteins and then use the last script
>>> mentioned above to add Dbxref and Ontology_term attributes to your
>>> GFF.
>>>
>>> Have a look at those scripts and then holler back if you have any
>>> questions or want more details.
>>>
>>> Barry
>>>
>>> On Nov 16, 2009, at 1:45 PM, Shane Brubaker wrote:
>>>
>>>> Hi, I had a couple of general questions.
>>>>
>>>> 1.  What are the EST blastn results that are found in the MAKER gff3
>>>> output?  I thought these might be a track of my ESTs mapped onto the
>>>> genome, but they seem to contain pieces of the EST but not the
>>>> entire thing?
>>>> 2.  What is a good way to add functional annotation to the gene
>>>> results? I have a track of protein matches, I used Swissprot as my
>>>> set of proteins.  So I can see proteins and I can look up my
>>>> Swissprot accession number and find out more about that gene.  But
>>>> what I really want is to click on my actual gene models (from
>>>> augustus or snap) and then have some functional annotation on that
>>>> page which has been transferred onto the gene, as well as some links
>>>> out to the appropriate external sites.  Is there a good general
>>>> approach for doing that?
>>>>
>>>>
>>>> Thanks,
>>>> Shane
>>>>
>>>> This email and any attachments thereto may contain private,
>>>> confidential, and privileged material for the sole use of the
>>>> intended recipient.  Any review, copying, or distribution of this
>>>> email (or any attachments thereto) by others is strictly
>>>> prohibited.  If you are not the intended recipient, please contact
>>>> the sender immediately and permanently delete the original and any
>>>> copies of this email and any attachments thereto.
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at yandell-lab.org
>>>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 3
>>> Date: Mon, 16 Nov 2009 15:41:19 -0800
>>> From: Shane Brubaker <SBrubaker at Aurorabiofuels.com>
>>> Subject: Re: [maker-devel] Question on ESTs and functional annotations
>>> To: Barry Moore <barry.moore at genetics.utah.edu>
>>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>>> Message-ID:
>>>      <4F28B35C91C1B040B7183D28726A8663264CEF1545 at Exchange.aurora.local
>>>>
>>> Content-Type: text/plain; charset="us-ascii"
>>>
>>> That is very helpful, thanks Barry!
>>>
>>> -----Original Message-----
>>> From: Barry Moore [mailto:barry.moore at genetics.utah.edu]
>>> Sent: Monday, November 16, 2009 2:35 PM
>>> To: Shane Brubaker
>>> Cc: maker-devel at yandell-lab.org
>>> Subject: Re: [maker-devel] Question on ESTs and functional annotations
>>>
>>> Shane,
>>>
>>> With regards to your second question...we've got a few scripts in the
>>> bin directory that we have used to add functional annotations to MAKER
>>> output.  They are:
>>>
>>> maker_functional_fasta
>>> maker_functional_gff
>>> ipr_update_gff
>>>
>>> The first two will take a blastp output from your MAKER proteins
>>> against swissprot and add this sort of thing:
>>>
>>> name:"Serine-aspartate repeat-containing protein I (Staphylococcus
>>> saprophyticus)"
>>> Note="Serine-aspartate repeat-containing protein I (Staphylococcus
>>> saprophyticus)"
>>>
>>> to your fasta and GFF files respectively.  It's not currently adding
>>> the swissprot ID to that output, but it would be trivial to alter
>>> either or both to do so.
>>>
>>> Also a great (but CPU costly) way to get deeper functional annotations
>>> is to run IPRscan on your MAKER proteins and then use the last script
>>> mentioned above to add Dbxref and Ontology_term attributes to your
>>> GFF.
>>>
>>> Have a look at those scripts and then holler back if you have any
>>> questions or want more details.
>>>
>>> Barry
>>>
>>> On Nov 16, 2009, at 1:45 PM, Shane Brubaker wrote:
>>>
>>>> Hi, I had a couple of general questions.
>>>>
>>>> 1.  What are the EST blastn results that are found in the MAKER gff3
>>>> output?  I thought these might be a track of my ESTs mapped onto the
>>>> genome, but they seem to contain pieces of the EST but not the
>>>> entire thing?
>>>> 2.  What is a good way to add functional annotation to the gene
>>>> results? I have a track of protein matches, I used Swissprot as my
>>>> set of proteins.  So I can see proteins and I can look up my
>>>> Swissprot accession number and find out more about that gene.  But
>>>> what I really want is to click on my actual gene models (from
>>>> augustus or snap) and then have some functional annotation on that
>>>> page which has been transferred onto the gene, as well as some links
>>>> out to the appropriate external sites.  Is there a good general
>>>> approach for doing that?
>>>>
>>>>
>>>> Thanks,
>>>> Shane
>>>>
>>>> This email and any attachments thereto may contain private,
>>>> confidential, and privileged material for the sole use of the
>>>> intended recipient.  Any review, copying, or distribution of this
>>>> email (or any attachments thereto) by others is strictly
>>>> prohibited.  If you are not the intended recipient, please contact
>>>> the sender immediately and permanently delete the original and any
>>>> copies of this email and any attachments thereto.
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at yandell-lab.org
>>>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>> This email and any attachments thereto may contain private,
>>> confidential, and privileged material for the sole use of the
>>> intended recipient.  Any review, copying, or distribution of this
>>> email (or any attachments thereto) by others is strictly
>>> prohibited.  If you are not the intended recipient, please contact
>>> the sender immediately and permanently delete the original and any
>>> copies of this email and any attachments thereto.
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 4
>>> Date: Mon, 16 Nov 2009 16:42:25 -0700
>>> From: Carson Holt <carson.holt at genetics.utah.edu>
>>> Subject: Re: [maker-devel] Question on ESTs and functional annotations
>>> To: Shane Brubaker <SBrubaker at Aurorabiofuels.com>,
>>>      "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>>> Message-ID: <C7273171.112B%carson.holt at genetics.utah.edu>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> 1. The BLASTN ESTs are the BLASTN results of aligning the EST
>>> library you provided during a MAKER run.  These are filtered using
>>> the thresholds you set in the maker_bopts.ctl file for coverage,
>>> identity, etc.  I think the default coverage is 80% and the default
>>> identity is 85%.  So all alignments should contain at least 80% of
>>> the EST provided with 85% identity.  You can tighten and loosen
>>> these thresholds as needed since you do expect a certain amount of
>>> sequencing error in the ESTs.
>>>
>>> Positive BLASTN results actually get realigned using Exonerate which
>>> gives a higher quality alignment that is splice site aware.  BLASTN
>>> alignments are recorded more for informative purposes.  The
>>> important alignments are actually the Exonerate est2genome
>>> alignments which are derived from the BLASTN alignments.  Note, you
>>> will sometimes see a BLASTN alignment on one strand while the
>>> Exonerate alignment will be on the other, this is because splice
>>> sites allow you to correctly determine the strand which is not
>>> actually inherent from the EST sequence (except for Sanger sequence).
>>>
>>> 2. For functional annotation, I like to use InterProScan from the
>>> EBI.  It can be used to identify protein domains and related GO
>>> functional categories for a gene.  InterProScan takes a while to run
>>> though, as it is an extremely extensive analysis.  The current
>>> version of MAKER includes a few accessory scripts for adding
>>> InterProScan results into the final annotation set.  The main script
>>> is ipr_update_gff.  It will add functional tags to the gene models
>>> in accordance to GFF3 format.  You can then dump these GFF3 files
>>> into a Chado database and run things like GBrowse off of it.
>>>
>>> If you are using GBrowse for viewing your data, you can set it up to
>>> link out to the appropriate external sites.  It is not entirely
>>> simple to do, but they do provide documentation.  You will also need
>>> to be familiar with SQL for some of the more advanced options.
>>>
>>> Hope that helps,
>>> Carson
>>>
>>>
>>>
>>> On 11/16/09 1:45 PM, "Shane Brubaker" <SBrubaker at Aurorabiofuels.com>
>>> wrote:
>>>
>>> Hi, I had a couple of general questions.
>>>
>>> 1.  What are the EST blastn results that are found in the MAKER gff3
>>> output?  I thought these might be a track of my ESTs mapped onto the
>>> genome, but they seem to contain pieces of the EST but not the
>>> entire thing?
>>> 2.  What is a good way to add functional annotation to the gene
>>> results? I have a track of protein matches, I used Swissprot as my
>>> set of proteins.  So I can see proteins and I can look up my
>>> Swissprot accession number and find out more about that gene.  But
>>> what I really want is to click on my actual gene models (from
>>> augustus or snap) and then have some functional annotation on that
>>> page which has been transferred onto the gene, as well as some links
>>> out to the appropriate external sites.  Is there a good general
>>> approach for doing that?
>>>
>>>
>>> Thanks,
>>> Shane
>>>
>>> This email and any attachments thereto may contain private,
>>> confidential, and privileged material for the sole use of the
>>> intended recipient.  Any review, copying, or distribution of this
>>> email (or any attachments thereto) by others is strictly
>>> prohibited.  If you are not the intended recipient, please contact
>>> the sender immediately and permanently delete the original and any
>>> copies of this email and any attachments thereto.
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at yandell-lab.org
>>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>> -------------- next part --------------
>>> An HTML attachment was scrubbed...
>>> URL:
>>> <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20091116/cf8876c2/attachment-0001.html
>>>>
>>>
>>> ------------------------------
>>>
>>> Message: 5
>>> Date: Mon, 16 Nov 2009 15:48:22 -0800
>>> From: Shane Brubaker <SBrubaker at Aurorabiofuels.com>
>>> Subject: Re: [maker-devel] Question on ESTs and functional annotations
>>> To: Carson Holt <carson.holt at genetics.utah.edu>,
>>>      "maker-devel at yandell-lab.org"   <maker-devel at yandell-lab.org>
>>> Message-ID:
>>>      <4F28B35C91C1B040B7183D28726A8663264CEF1547 at Exchange.aurora.local
>>>>
>>> Content-Type: text/plain; charset="us-ascii"
>>>
>>> Thanks very much Carson, that is quite helpful.  I will try using
>>> the est2genome results instead of the blastn results.
>>>
>>> I am indeed using Chado and Gbrowse, so that is what I would like to
>>> do.  I will try using InterproScan.
>>>
>>>
>>> From: Carson Holt [mailto:carson.holt at genetics.utah.edu]
>>> Sent: Monday, November 16, 2009 3:42 PM
>>> To: Shane Brubaker; maker-devel at yandell-lab.org
>>> Subject: Re: [maker-devel] Question on ESTs and functional annotations
>>>
>>> 1. The BLASTN ESTs are the BLASTN results of aligning the EST
>>> library you provided during a MAKER run.  These are filtered using
>>> the thresholds you set in the maker_bopts.ctl file for coverage,
>>> identity, etc.  I think the default coverage is 80% and the default
>>> identity is 85%.  So all alignments should contain at least 80% of
>>> the EST provided with 85% identity.  You can tighten and loosen
>>> these thresholds as needed since you do expect a certain amount of
>>> sequencing error in the ESTs.
>>>
>>> Positive BLASTN results actually get realigned using Exonerate which
>>> gives a higher quality alignment that is splice site aware.  BLASTN
>>> alignments are recorded more for informative purposes.  The
>>> important alignments are actually the Exonerate est2genome
>>> alignments which are derived from the BLASTN alignments.  Note, you
>>> will sometimes see a BLASTN alignment on one strand while the
>>> Exonerate alignment will be on the other, this is because splice
>>> sites allow you to correctly determine the strand which is not
>>> actually inherent from the EST sequence (except for Sanger sequence).
>>>
>>> 2. For functional annotation, I like to use InterProScan from the
>>> EBI.  It can be used to identify protein domains and related GO
>>> functional categories for a gene.  InterProScan takes a while to run
>>> though, as it is an extremely extensive analysis.  The current
>>> version of MAKER includes a few accessory scripts for adding
>>> InterProScan results into the final annotation set.  The main script
>>> is ipr_update_gff.  It will add functional tags to the gene models
>>> in accordance to GFF3 format.  You can then dump these GFF3 files
>>> into a Chado database and run things like GBrowse off of it.
>>>
>>> If you are using GBrowse for viewing your data, you can set it up to
>>> link out to the appropriate external sites.  It is not entirely
>>> simple to do, but they do provide documentation.  You will also need
>>> to be familiar with SQL for some of the more advanced options.
>>>
>>> Hope that helps,
>>> Carson
>>>
>>>
>>>
>>> On 11/16/09 1:45 PM, "Shane Brubaker" <SBrubaker at Aurorabiofuels.com>
>>> wrote:
>>> Hi, I had a couple of general questions.
>>>
>>> 1.  What are the EST blastn results that are found in the MAKER gff3
>>> output?  I thought these might be a track of my ESTs mapped onto the
>>> genome, but they seem to contain pieces of the EST but not the
>>> entire thing?
>>> 2.  What is a good way to add functional annotation to the gene
>>> results? I have a track of protein matches, I used Swissprot as my
>>> set of proteins.  So I can see proteins and I can look up my
>>> Swissprot accession number and find out more about that gene.  But
>>> what I really want is to click on my actual gene models (from
>>> augustus or snap) and then have some functional annotation on that
>>> page which has been transferred onto the gene, as well as some links
>>> out to the appropriate external sites.  Is there a good general
>>> approach for doing that?
>>>
>>>
>>> Thanks,
>>> Shane
>>>
>>> This email and any attachments thereto may contain private,
>>> confidential, and privileged material for the sole use of the
>>> intended recipient.  Any review, copying, or distribution of this
>>> email (or any attachments thereto) by others is strictly
>>> prohibited.  If you are not the intended recipient, please contact
>>> the sender immediately and permanently delete the original and any
>>> copies of this email and any attachments thereto.
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at yandell-lab.org
>>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>> -------------- next part --------------
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>>>>
>>>
>>> ------------------------------
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at yandell-lab.org
>>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>> End of maker-devel Digest, Vol 18, Issue 4
>>> ******************************************
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at yandell-lab.org
>>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> This email and any attachments thereto may contain private, confidential,
>> and privileged material for the sole use of the intended recipient.  Any
>> review, copying, or distribution of this email (or any attachments thereto)
>> by others is strictly prohibited.  If you are not the intended recipient,
>> please contact the sender immediately and permanently delete the original
>> and any copies of this email and any attachments thereto.
>
>
> _______________________________________________
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research