[maker-devel] ipr_update_gff
Barry Moore
barry.moore at genetics.utah.edu
Wed Nov 18 21:48:32 MST 2009
Thanks Scott. Shane, I'd suggest you have a look back through the
GBrowse/Chado docs on these callbacks and then hit up the GBrowse list
for further clarification. We certainly don't mind the Gbrowse/Chado
discussion on this list, but you might have a wider pool of
experienced users over there. Your welcome to cross post here as well
- it's a good discussion for the MAKER archives 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 9:39 PM, Scott Cain wrote:
> 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 --------------
>>>> An HTML attachment was scrubbed...
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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.
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at yandell-lab.org
>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. scott at
> scottcain dot net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
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