ValWood
commented
5 years ago We need to do a few things here:
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[x] 1. Add links to resources that provide trees and alignments https://github.com/pombase/website/issues/1241
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[x] 2. Make users aware that these links are in the external section (suggestion below). I plan to mail users to explain this, but maybe we should also include in the ortholog section (discuss tomorrow). Label the ortholog section clearly "manually assigned orthologs"
So the section could extend: Manually assigned orthologs
Predicted orthologs @kimrutherford will duplicate the ortholgo links in this section
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[x] 3. Improve FAQs. FAQ link for https://www.pombase.org/documentation/orthologs to FAQ on orthologs in additional species. is broken
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[ ] 4. Add a web service for orthologs in the longer term https://github.com/pombase/website/issues/33
mah11
Lots of comments/request relating to about orthologs and alignments
ORTHOLOGS and ALIGNMENT I would like the 'ortholog' section to be expanded to include more species, particularly other fungal model organisms. E.g. S. japonicus, N. crassa, A. nidulans, A. gossypii. information on orthologs Possible tools that enable quick inverse search for pombe homolog. Searching orthologs Orthology and human disease Data for homologues/orhtologues in other organisms More description for orthologues homolog list More information about ortholog functions protein homology with other organisms homology info in other organisms a link to other organisms' (especially humans') gene products links to other fungal protein databases. eg. homologue alignment across many yeasts (not just fission plus S. cerevisiae). Fungal pathogens. I'd appreciate more ways to identify homologs/link out to existing orthology databases/ integrate with phylogenetic analyses of fungi and other eukaryotes Relationship to higher eukaryotic proteins and complexes Based on my memory, I used to like the older version of Pombase for looking at homologs/orthologs--I think this used to show more information than it does currently, and even some limited alignment (I htink it was pink in those days) Relationship to higher eukaryotic proteins and complexes orthology links with Wormbase so it is easier to identify pombe homolog of C. elegans gene and vice versa. new tools to check protein sequence structure and its alignments in other organisms gene function linked with mammalian cells druggable (homologs in human, fungi, etc) or not. OTHEr FISSION YEAST Compare fission yeast gene with gene from other yeasts link to other fission yeast species Please inlcude the datasets of the other fission yeast species. More comparative tools (synteny, multiple alignment, gene family trees, etc.) with the other Schizo genomes.
other schizos/ alignments 3 Pre-computed protein sequence alignments or pre-computed BLAST results (like the discontinued NCBI BLink)