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PomBase website v2
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new submit option for sequence searches #1780

Closed ValWood closed 2 years ago

ValWood commented 2 years ago

Is it possible to send sequences directly to https://www.ebi.ac.uk/Tools/hmmer/search/jackhmmer and https://www.ebi.ac.uk/Tools/sss/fasta/ directly from the sequence section as we do for blast?

I use these the most these days for distant ortholog detection. I think others would find them useful as it will be a long time before I can work through all unconserved, or taxon restricted.

kimrutherford commented 2 years ago

I was able to add a button for jackhmmer (which is working on pombase.org) but not for FASTA. I'll look harder on Monday.

ValWood commented 2 years ago

OK, no worries if it isn't 'easy'. I will announce this because these are the best 2 methods to identify the remaining distant orthologs.

kimrutherford commented 2 years ago

but not for FASTA. I'll look harder on Monday.

I can't see a way to auto-fill the sequence box on the FASTA server page.

ValWood commented 2 years ago

OK I will request that the EBI provide that.... But this can close.

ValWood commented 2 years ago

message sent: From PomBase we provide links to auto-populate a sequence search box from the sequence section of gene pages. We provide this for Ensembl blase, NCBIblast, jackhammer, but we could not see a way to do this for the FASTA server.

Would it be possible to make this option available in the future? I find FASTA one of the most useful searches for refining gene structures and the identification of distant orthologs. I think our users would benefit from it's inclusion.