(M) Protein domain and other protein annotation from Uniprot (fast/medium, needs A,B)

[mrshu]

• The uniprot database (http://www.uniprot.org/) contains information about proteins. The goal is to download information about malGlo and malSym proteins, parse out info about particular regions and map these to the corresponding regions of the genome.
• See sacCer3 tracks Pfam (L), uniProtAnnot (L), uniProtStruct (L)
• Download protein info in XML format malGlo [5], malSym [6]
• Last year's protocol links uniprot proteins to genes from browser annotation via sequence similarity search (blat). Possibly this could be done also by cross-linking information from the databases, but blat is fine.
• https://github.com/fmfi-genomika/genomika-2017/wiki/Uniprot-data
• Last year, Pfam track was created by runing Interproscan tool locally [7]. However, this is time-consuming and uniprot contains pre-computed info about Pfam domains. Therefore it would be better to modify scripts so that they parse Pfam out of uniprot XML files together with other info.

[bbrejova]

The second group has realized that XML file from uniprot does not contain domain positions for Pfam. Therefore for Pfam you need to download a file directly from Pfam database. MalGlo page is here: http://pfam.xfam.org/proteome/425265 and within there download Domain composition ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/proteomes/425265.tsv.gz

[bbrejova]

I would change the default setting for these tracks from "full", which takes a lot of space on the screen to "pack" or even "hide"