[ensembl-dev] Dev Digest, Vol 29, Issue 18
Javier Herrero
jherrero at ebi.ac.uk
Mon Nov 19 15:54:17 GMT 2012
Dear Pierre
I am not sure I fully understand the nature of your question. Would you
be kind enough to elaborate a little more and tell us which alternatives
you refer to and what is your aim?
Kind regards
Javier
On 15/11/12 21:23, pierre devaux wrote:
> This is not clear to me what to do with those alternatives. Please let me know more.
> Thks,
> P Devaux
>
> -----Message d'origine-----
> De : dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] De la part de dev-request at ensembl.org
> Envoyé : jeudi 15 novembre 2012 12:06
> À : dev at ensembl.org
> Objet : Dev Digest, Vol 29, Issue 18
>
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> Today's Topics:
>
> 1. which version of genome to use fro RNA-seq mapping (Julien Roux)
> 2. Re: EnsEMBL compara / protein sequence alignments (Javier Herrero)
> 3. Converting cDNA position to genomic position!
> (Oyediran Akinrinade)
> 4. Re: Converting cDNA position to genomic position! (Will McLaren)
> 5. Re: EnsEMBL compara / protein sequence alignments (Graham Ritchie)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 14 Nov 2012 15:08:39 -0600
> From: Julien Roux <julien.roux at unil.ch>
> Subject: [ensembl-dev] which version of genome to use fro RNA-seq
> mapping
> To: dev at ensembl.org
> Message-ID: <50A40857.5020001 at unil.ch>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear Ensembl team,
> I am aiming at mapping RNA-seq reads to the human genome using tophat, however I am unsure which version of the genome I should use to do this.
>
> After some searches I have seen that people tend to use the non-masked "toplevel" version of the genome (ftp://ftp.ensembl.org/pub/release-69/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.69.dna.toplevel.fa.gz),
> but I am wondering if this is a good idea: because of the redundant sequences found in the patches, the aligner will conclude that some reads map at multiple locations and these reads will be discarded.
>
> Another option would be to map to the "primary assembly"
> (ftp://ftp.ensembl.org/pub/release-69/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.69.dna.primary_assembly.fa.gz),
> but this ignores some of recent improvements to the genome (fix patches).
>
> Ideally I would like to use a "golden path" assembly (sum of all top-level sequences, omitting any redundant regions). What would you suggest?
> Thanks
> Julien
>
> --
> Julien Roux, PhD
> Gilad lab, Department of Human Genetics, University of Chicago http://giladlab.uchicago.edu/
> 920 East 58th Street, CLSC 317, Chicago, IL 60637, USA
> tel: +1-773-834-1984 fax: +1-773-834-8470
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 15 Nov 2012 11:34:18 +0900
> From: Javier Herrero <jherrero at ebi.ac.uk>
> Subject: Re: [ensembl-dev] EnsEMBL compara / protein sequence
> alignments
> To: dev at ensembl.org
> Message-ID: <50A454AA.6050900 at ebi.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
> Hi Sabrina
>
> I see. We have been considering using the family alignments for SIFT as
> well. You can get the alignments from the families, you don't need to
> re-align the proteins. Ensembl families contain very closely-related
> proteins.
>
> The script you need to get the alignment from a family is fairly simple
> and we can help you with this. Is there any reason why you want to
> restrict your analysis to a given set of genomes? Would you consider
> using all proteins in the family (again, they are all very similar
> proteins)?
>
> Javier
>
> On 14/11/12 17:25, srodriguez wrote:
>> Hi Javier,
>>
>> Actually, we would like to obtain alignments of orthologous proteins
>> isoforms.
>> These alignments would be used as entries for SIFT program.
>>
>> After testing different methods (families...), I am still not sure
>> about the best way to get these alignments with Ensembl...
>>
>> I am thinking about starting from genes from my query specie. For each
>> query specie gene, I would get all orthologs genes from my "hit
>> species" and then get all their proteins. Then I would align these
>> proteins to get orthologous proteins isoforms.
>>
>> What do you think about this eventual method?
>>
>> Best regards,
>>
>> Sabrina.
>>
>>
>> Javier Herrero <jherrero at ebi.ac.uk> a ?crit :
>>
>>> BTW, we have an example script
>>> (ensembl-compara/scripts/examples/families_workshop_fetchFamilyAlignment.pl)
>>> that does something very similar to what you want (but just for one
>>> gene).
>>>
>>> Javier
>>>
>>> On 07/11/12 11:25, Javier Herrero wrote:
>>>> Hi Sabrina
>>>>
>>>> It is certainly possible to get proteins from several species.
>>>>
>>>> If you are interested in getting alignments for all possible
>>>> isoforms (each possible protein from each gene), you would have to
>>>> use the Ensembl families. These are groups of similar proteins, but
>>>> you should not assume that they are all orthologues. To infer
>>>> orthology, you need a phylogenetic tree. The trees we provide are
>>>> built using only one single representative protein per gene.
>>>>
>>>> In your case, I would recommend to use the Ensembl families, query
>>>> the families using each cow (this is you query species, isn't it?)
>>>> protein and dump the alignments. There are several options for this.
>>>> You may want to use all possible species (the families are built
>>>> using Ensembl and non-Ensembl proteins) or limit the alignment to a
>>>> subset of species. Also, in some cases you will find that more than
>>>> one cow proteins are in the same family, so you will get duplicated
>>>> alignments. Is this OK?
>>>>
>>>> Kind regards
>>>>
>>>> Javier
>>>>
>>>> On 05/11/12 13:47, srodriguez wrote:
>>>>> Hi Javier,
>>>>>
>>>>> Thank you for your answer.
>>>>>
>>>>> Actually, I would like to obtain, 1 file per protein query aligned
>>>>> to all other species ortholog proteins (and not 1 sequence to 1
>>>>> sequence).
>>>>>
>>>>> ex:
>>>>> for protein ENSBTAP00000032594, the file containing:
>>>>> ENSBTAP00000032594/1-397
>>>>> MDALRASAAKPPTGRKMKARAPPPPGKPATPNLHSGQRSPRRASPGPPQNQLSR
>>>>> ENSP00000265136/1-1261
>>>>> MDAPRASAAKPPTGRKMKARAPPPPGKAATLHVHSDQKPPHDGALGSQQNLVRMK
>>>>> ENSSPECIE2...
>>>>> ENSSPECIE3...
>>>>> *** ***********************.** ::**.*:.*:
>>>>> .: *. ** :
>>>>>
>>>>> Also, I would like to have 1 file per protein from the query, and
>>>>> if a gene has several proteins, obtain all the proteins query as
>>>>> single files with the alignment as above.
>>>>>
>>>>> Do you know if it is feasible to obtain such an output with Ensembl
>>>>> compara?
>>>>>
>>>>> In that case, could you please modify the script to obtain it?
>>>>>
>>>>> Thank you very much in advance.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Sabrina.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Javier Herrero <jherrero at ebi.ac.uk> a ?crit :
>>>>>
>>>>>> Dear Sabrina
>>>>>>
>>>>>> I have modified the script slightly only. Essentially, I have
>>>>>> removed some bits that were not required and cleaned up the code a
>>>>>> little. I have also added the possibility of specifying the query
>>>>>> and the target species in the command line. Last, I have also
>>>>>> changed the script to output the alignments into separate files.
>>>>>>
>>>>>> Your strategy using the ENSEMBLGENE was correct. Indeed, you get
>>>>>> two proteins aligned. I believe this is what you want, isn't it?
>>>>>>
>>>>>> I have added a few comments. Let me know if there something that
>>>>>> is not clear.
>>>>>>
>>>>>> Javier
>>>>>>
>>>>>> On 22/10/12 15:58, srodriguez wrote:
>>>>>>> Dear all,
>>>>>>>
>>>>>>> I would like to use compara EnsEMBL API to get the aligned
>>>>>>> protein sequences of a query animal with homologous protein
>>>>>>> sequences from other species.
>>>>>>>
>>>>>>> The script would take as input the query specie name, (and if
>>>>>>> possible the hit species names). The script would get the
>>>>>>> proteins of the query organism, then the homologous protein
>>>>>>> sequences, and then retrieves 1 file per protein query sequence
>>>>>>> containing the alignment of the query (placed as the first
>>>>>>> sequence) and then the other specie protein sequences aligned.
>>>>>>>
>>>>>>> I was thinking about using an "homology adaptor" with ENSEMBLPEP,
>>>>>>> so I started a script that way, but I do not obtain any results
>>>>>>> with ENSEMBLPEP and the results with ENSEMBLGENE are 2 sequences
>>>>>>> per alignment (see script attached).
>>>>>>>
>>>>>>> I also tried with "families", but sometimes, I do not get the
>>>>>>> protein sequence for my specie query in the sequence alignment
>>>>>>> even though I searched by using my taxon id (script N#2 attached).
>>>>>>>
>>>>>>> Would you have a script that already performs my goal?
>>>>>>>
>>>>>>> If not, could you please help me reaching my goal?
>>>>>>>
>>>>>>> Thank you very much in advance.
>>>>>>>
>>>>>>> Best regards,
>>>>>>>
>>>>>>> Sabrina.
>>>>>>>
>>>>>>>
>>>>>>> *******************************************
>>>>>>> Sabrina Rodriguez
>>>>>>> Bioinformatics
>>>>>>> D?partement de G?n?tique animale
>>>>>>> Unit? GABI
>>>>>>> Domaine de Vilvert
>>>>>>> 78532 Jouy en josas
>>>>>>>
>>>>>>> +33 (0) 1 34 65 29 53
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>> --
>>>>>> Javier Herrero, PhD
>>>>>> Ensembl Coordinator and Ensembl Compara Project Leader
>>>>>> European Bioinformatics Institute (EMBL-EBI)
>>>>>> Wellcome Trust Genome Campus, Hinxton
>>>>>> Cambridge - CB10 1SD - UK
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> *******************************************
>>>>> Sabrina Rodriguez
>>>>> Bioinformatics
>>>>> D?partement de G?n?tique animale
>>>>> Unit? GABI
>>>>> Domaine de Vilvert
>>>>> 78532 Jouy en josas
>>>>>
>>>>> +33 (0) 1 34 65 29 53
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing listDev at ensembl.org
>>>>> Posting guidelines and subscribe/unsubscribe
>>>>> info:http://lists.ensembl.org/mailman/listinfo/dev
>>>>> Ensembl Blog:http://www.ensembl.info/
>>>> --
>>>> Javier Herrero, PhD
>>>> Ensembl Coordinator and Ensembl Compara Project Leader
>>>> European Bioinformatics Institute (EMBL-EBI)
>>>> Wellcome Trust Genome Campus, Hinxton
>>>> Cambridge - CB10 1SD - UK
>>> --
>>> Javier Herrero, PhD
>>> Ensembl Coordinator and Ensembl Compara Project Leader
>>> European Bioinformatics Institute (EMBL-EBI)
>>> Wellcome Trust Genome Campus, Hinxton
>>> Cambridge - CB10 1SD - UK
>>>
>>>
>>
>>
>>
>> *******************************************
>> Sabrina Rodriguez
>> Bioinformatics
>> D?partement de G?n?tique animale
>> Unit? GABI
>> Domaine de Vilvert
>> 78532 Jouy en josas
>>
>> +33 (0) 1 34 65 29 53
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
> --
> Javier Herrero, PhD
> Ensembl Coordinator and Ensembl Compara Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge - CB10 1SD - UK
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 15 Nov 2012 12:45:24 +0200
> From: "Oyediran Akinrinade" <oyediran.akinrinade at helsinki.fi>
> Subject: [ensembl-dev] Converting cDNA position to genomic position!
> To: dev at ensembl.org
> Message-ID:
> <20121115124524.20802ky3bs0wrcg4.akinrina at webmail.helsinki.fi>
> Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed"
>
>
>
> Hello,
>
> I have a list of ensembl transcripts IDs with their corresponding cDNA
> positions and I will like to get their genomic positions using the
> ensembl API. I have no experience with perl although I have
> installed ensembl-api on my mac computer. There are about 6000 IDs
> that I will like to get their genomic cordinates/positions, and
> web-based queries will not be the best solution. To this end, I
> write to request for your assistance.
>
> Looking forward to hearing from you soonest.
>
> Thanks,
>
> -Oyediran
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 15 Nov 2012 10:59:56 +0000
> From: Will McLaren <wm2 at ebi.ac.uk>
> Subject: Re: [ensembl-dev] Converting cDNA position to genomic
> position!
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID:
> <CAMVEDX1GCeL7-Ko-p0avEHvuJkq9G6YVe2SsEV940hcasntG-w at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello Oyediran,
>
> You will need to use a TranscriptMapper object;
> http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1TranscriptMapper.html
>
> The method you should use is cdna2genomic. Note that this returns an array
> of coordinate objects; this is useful to know if, for example, your
> coordinates only partially overlap the transcript.
>
> Here's a bit of code to get you started:
>
> my $reg = 'Bio::EnsEMBL::Registry';
> $reg->load_registry_from_db(-host => 'ensembldb.ensembl.org',-user =>
> 'anonymous');
>
> my $ta = $reg->get_adaptor('human','core','transcript');
>
> my $t = $ta->fetch_by_stable_id('ENST00000373968');
>
> my $mapper = Bio::EnsEMBL::TranscriptMapper->new($t);
>
> @coords = $trmapper->cdna2genomic( 123, 554 );
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
>
> On 15 November 2012 10:45, Oyediran Akinrinade <
> oyediran.akinrinade at helsinki.fi> wrote:
>
>>
>> Hello,
>>
>> I have a list of ensembl transcripts IDs with their corresponding cDNA
>> positions and I will like to get their genomic positions using the
>> ensembl API. I have no experience with perl although I have
>> installed ensembl-api on my mac computer. There are about 6000 IDs
>> that I will like to get their genomic cordinates/positions, and
>> web-based queries will not be the best solution. To this end, I
>> write to request for your assistance.
>>
>> Looking forward to hearing from you soonest.
>>
>> Thanks,
>>
>> -Oyediran
>>
>>
>>
>>
>>
>> ______________________________**_________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/**mailman/listinfo/dev<http://lists.ensembl.org/mailman/listinfo/dev>
>> Ensembl Blog: http://www.ensembl.info/
>>
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 5
> Date: Thu, 15 Nov 2012 11:06:03 +0000
> From: Graham Ritchie <grsr at ebi.ac.uk>
> Subject: Re: [ensembl-dev] EnsEMBL compara / protein sequence
> alignments
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID: <6C1C70FF-475A-4D98-8AF3-D2A947556BEB at ebi.ac.uk>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi Sabrina,
>
> There is in fact some code in the Variation API that will fetch the appropriate Compara family for a given protein ID and then create an alignment file in the format expected by SIFT. Have a look at the dump_alignment_for_sift subroutine in the Bio::EnsEMBL::Variation::Utils::ComparaUtils module, documentation here:
>
> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Utils_1_1ComparaUtils.html
>
> If you do need to restrict the alignment to certain species you could probably adapt this code to do so.
>
> Cheers,
>
> Graham
>
>
> On 15 Nov 2012, at 02:34, Javier Herrero <jherrero at ebi.ac.uk> wrote:
>
>> Hi Sabrina
>>
>> I see. We have been considering using the family alignments for SIFT as well. You can get the alignments from the families, you don't need to re-align the proteins. Ensembl families contain very closely-related proteins.
>>
>> The script you need to get the alignment from a family is fairly simple and we can help you with this. Is there any reason why you want to restrict your analysis to a given set of genomes? Would you consider using all proteins in the family (again, they are all very similar proteins)?
>>
>> Javier
>>
>> On 14/11/12 17:25, srodriguez wrote:
>>> Hi Javier,
>>>
>>> Actually, we would like to obtain alignments of orthologous proteins isoforms.
>>> These alignments would be used as entries for SIFT program.
>>>
>>> After testing different methods (families...), I am still not sure about the best way to get these alignments with Ensembl...
>>>
>>> I am thinking about starting from genes from my query specie. For each query specie gene, I would get all orthologs genes from my "hit species" and then get all their proteins. Then I would align these proteins to get orthologous proteins isoforms.
>>>
>>> What do you think about this eventual method?
>>>
>>> Best regards,
>>>
>>> Sabrina.
>>>
>>>
>>> Javier Herrero <jherrero at ebi.ac.uk> a ?crit :
>>>
>>>> BTW, we have an example script (ensembl-compara/scripts/examples/families_workshop_fetchFamilyAlignment.pl) that does something very similar to what you want (but just for one gene).
>>>>
>>>> Javier
>>>>
>>>> On 07/11/12 11:25, Javier Herrero wrote:
>>>>> Hi Sabrina
>>>>>
>>>>> It is certainly possible to get proteins from several species.
>>>>>
>>>>> If you are interested in getting alignments for all possible isoforms (each possible protein from each gene), you would have to use the Ensembl families. These are groups of similar proteins, but you should not assume that they are all orthologues. To infer orthology, you need a phylogenetic tree. The trees we provide are built using only one single representative protein per gene.
>>>>>
>>>>> In your case, I would recommend to use the Ensembl families, query the families using each cow (this is you query species, isn't it?) protein and dump the alignments. There are several options for this. You may want to use all possible species (the families are built using Ensembl and non-Ensembl proteins) or limit the alignment to a subset of species. Also, in some cases you will find that more than one cow proteins are in the same family, so you will get duplicated alignments. Is this OK?
>>>>>
>>>>> Kind regards
>>>>>
>>>>> Javier
>>>>>
>>>>> On 05/11/12 13:47, srodriguez wrote:
>>>>>> Hi Javier,
>>>>>>
>>>>>> Thank you for your answer.
>>>>>>
>>>>>> Actually, I would like to obtain, 1 file per protein query aligned to all other species ortholog proteins (and not 1 sequence to 1 sequence).
>>>>>>
>>>>>> ex:
>>>>>> for protein ENSBTAP00000032594, the file containing:
>>>>>> ENSBTAP00000032594/1-397 MDALRASAAKPPTGRKMKARAPPPPGKPATPNLHSGQRSPRRASPGPPQNQLSR
>>>>>> ENSP00000265136/1-1261 MDAPRASAAKPPTGRKMKARAPPPPGKAATLHVHSDQKPPHDGALGSQQNLVRMK
>>>>>> ENSSPECIE2...
>>>>>> ENSSPECIE3...
>>>>>> *** ***********************.** ::**.*:.*: .: *. ** :
>>>>>>
>>>>>> Also, I would like to have 1 file per protein from the query, and if a gene has several proteins, obtain all the proteins query as single files with the alignment as above.
>>>>>>
>>>>>> Do you know if it is feasible to obtain such an output with Ensembl compara?
>>>>>>
>>>>>> In that case, could you please modify the script to obtain it?
>>>>>>
>>>>>> Thank you very much in advance.
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Sabrina.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Javier Herrero <jherrero at ebi.ac.uk> a ?crit :
>>>>>>
>>>>>>> Dear Sabrina
>>>>>>>
>>>>>>> I have modified the script slightly only. Essentially, I have removed some bits that were not required and cleaned up the code a little. I have also added the possibility of specifying the query and the target species in the command line. Last, I have also changed the script to output the alignments into separate files.
>>>>>>>
>>>>>>> Your strategy using the ENSEMBLGENE was correct. Indeed, you get two proteins aligned. I believe this is what you want, isn't it?
>>>>>>>
>>>>>>> I have added a few comments. Let me know if there something that is not clear.
>>>>>>>
>>>>>>> Javier
>>>>>>>
>>>>>>> On 22/10/12 15:58, srodriguez wrote:
>>>>>>>> Dear all,
>>>>>>>>
>>>>>>>> I would like to use compara EnsEMBL API to get the aligned protein sequences of a query animal with homologous protein sequences from other species.
>>>>>>>>
>>>>>>>> The script would take as input the query specie name, (and if possible the hit species names). The script would get the proteins of the query organism, then the homologous protein sequences, and then retrieves 1 file per protein query sequence containing the alignment of the query (placed as the first sequence) and then the other specie protein sequences aligned.
>>>>>>>>
>>>>>>>> I was thinking about using an "homology adaptor" with ENSEMBLPEP, so I started a script that way, but I do not obtain any results with ENSEMBLPEP and the results with ENSEMBLGENE are 2 sequences per alignment (see script attached).
>>>>>>>>
>>>>>>>> I also tried with "families", but sometimes, I do not get the protein sequence for my specie query in the sequence alignment even though I searched by using my taxon id (script N#2 attached).
>>>>>>>>
>>>>>>>> Would you have a script that already performs my goal?
>>>>>>>>
>>>>>>>> If not, could you please help me reaching my goal?
>>>>>>>>
>>>>>>>> Thank you very much in advance.
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>>
>>>>>>>> Sabrina.
>>>>>>>>
>>>>>>>>
>>>>>>>> *******************************************
>>>>>>>> Sabrina Rodriguez
>>>>>>>> Bioinformatics
>>>>>>>> D?partement de G?n?tique animale
>>>>>>>> Unit? GABI
>>>>>>>> Domaine de Vilvert
>>>>>>>> 78532 Jouy en josas
>>>>>>>>
>>>>>>>> +33 (0) 1 34 65 29 53
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>> --
>>>>>>> Javier Herrero, PhD
>>>>>>> Ensembl Coordinator and Ensembl Compara Project Leader
>>>>>>> European Bioinformatics Institute (EMBL-EBI)
>>>>>>> Wellcome Trust Genome Campus, Hinxton
>>>>>>> Cambridge - CB10 1SD - UK
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> *******************************************
>>>>>> Sabrina Rodriguez
>>>>>> Bioinformatics
>>>>>> D?partement de G?n?tique animale
>>>>>> Unit? GABI
>>>>>> Domaine de Vilvert
>>>>>> 78532 Jouy en josas
>>>>>>
>>>>>> +33 (0) 1 34 65 29 53
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Dev mailing listDev at ensembl.org
>>>>>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>>>>> Ensembl Blog:http://www.ensembl.info/
>>>>> --
>>>>> Javier Herrero, PhD
>>>>> Ensembl Coordinator and Ensembl Compara Project Leader
>>>>> European Bioinformatics Institute (EMBL-EBI)
>>>>> Wellcome Trust Genome Campus, Hinxton
>>>>> Cambridge - CB10 1SD - UK
>>>> --
>>>> Javier Herrero, PhD
>>>> Ensembl Coordinator and Ensembl Compara Project Leader
>>>> European Bioinformatics Institute (EMBL-EBI)
>>>> Wellcome Trust Genome Campus, Hinxton
>>>> Cambridge - CB10 1SD - UK
>>>>
>>>>
>>>
>>>
>>>
>>> *******************************************
>>> Sabrina Rodriguez
>>> Bioinformatics
>>> D?partement de G?n?tique animale
>>> Unit? GABI
>>> Domaine de Vilvert
>>> 78532 Jouy en josas
>>>
>>> +33 (0) 1 34 65 29 53
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>> --
>> Javier Herrero, PhD
>> Ensembl Coordinator and Ensembl Compara Project Leader
>> European Bioinformatics Institute (EMBL-EBI)
>> Wellcome Trust Genome Campus, Hinxton
>> Cambridge - CB10 1SD - UK
>>
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
>
>
> ------------------------------
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
> End of Dev Digest, Vol 29, Issue 18
> ***********************************
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
--
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK
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