[ensembl-dev] Question about Supporting evidence / Core API

[Thibaut Hourlier]

Hi Marc,
We have different type of supporting evidence for our models:
- transcript supporting evidence: it means that this evidence is covering the entire transcript. You can retrieve them the way you did with: $transcript_adaptor->fetch_all_by_transcript_supporting_evidence
- exon supporting evidence: it means that the sequence is covering only few exons of the transcript
- intron supporting evidence: it gives you the coverage of RNASeq reads spanning a splice site. You will only have this if the model was build using RNASeq data

If your sequence is stored as an exon supporting evidence you will not get it using $transcript_adaptor->fetch_all_by_transcript_supporting_evidence but you will need to use more code. Something like that:
my $feature = $protein_align_feature_adaptor->fetch_by_hitname("A0M8Q6");
my $slice = $feature->feature_Slice()
# Unless I'm wrong feature_Slice is "strand specific" so all objects on the same stand than your protein (feature) will be considered on the forward strand.
my $transcripts = $slice->fetch_all_Transcripts()
# work on the transcripts

Hope this helps
Thibaut

> On 23 Jun 2015, at 13:00, Healy, Matthew <Matthew.Healy at bms.com> wrote:
> 
> The simplest way I know of to obtain these mappings is to download one of the ID mapping files provided on the Uniprot web site and documented here:
> ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/README
> 
> In particular, the idmapping_selected.tab file for your species of interest gives mappings to Ensembl Gene, Transcript, and Protein identifiers.
> 
> 
> Uniprot and Swissprot identifiers are among the available choices for External ID in Biomart on the Ensembl side, but I have found the Uniprot mappings file very convenient because it gives a large number
>  of other identifiers that I frequently encounter.
> 
> 
> 
> Another extremely useful download, if you are working with human genes, is at HGNC:
> http://www.genenames.org/help/download
> This gives Ensembl and Uniprot identifiers, as does the Uniprot download.  The HGNC download also has some extremely useful content that is not readily available elsewhere, such as previously-approved HGNC symbols and synonyms.  I have found the synonyms and previous symbols fields from HGNC of great value for mapping lists of identifiers from sources that failed to use current approved symbols with consistency.  However, I also find that mappings based on synonyms require human checking before they can be trusted, because more than one gene may have the same synonym.
> 
> 
> From: dev-bounces at ensembl.org <dev-bounces at ensembl.org> on behalf of Marc P. Hoeppner <mphoeppner at gmail.com>
> Sent: Tuesday, June 23, 2015 6:42 AM
> To: dev at ensembl.org
> Subject: [ensembl-dev] Question about Supporting evidence / Core API
>  
> Dear EnsEMBL team,
> 
> Using EnsEMBL 79, I am trying to generate a best-guess mapping between Uniprot accession numbers and EnsEMBL transcripts. First, I tried:
> 
> fetch_all_by_external_name ()
> 
> But I noticed that this was leaving a lot of Uniprot accessions unmapped. I then checked on the website and found that these Uniprot accession tend to come up as "Supporting evidence". However, trying 
> 
> my $transcripts = $transcript_adaptor->fetch_all_by_transcript_supporting_evidence($accession,"protein_align_feature");
> 
> didn't seem to work. I am probably missing something about how this data is connected internally - are there feature sources other than "protein_align_feature" and "dna_align_feature", or does this connect via another adapter?
> 
> An example where this is not working for me would be Uniprot entry A0M8Q6 
> 
> Kind regards,
> 
> Marc
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