RdRp Explorer - Search by palmID

[ababaian]

Currently the RdRp Explorer page allows for searching by Virus Family, Genbank ID, or SRA Accession Code.

It is useful to search in which datasets a specific RdRp sequence occurs, BLAST-like search is one obvious feature (implemented in palmID) but a simpler interface would be the ability to retrieve all datasets in which a given palmprint sequence occurs in.

This information is already stored on the SQL server in the palm_sra Table. So one could query for a given palm_id (palmprint accession code) and get the SRA accession codes.

For example to find u1337 and u43110 you can search those codes with

where palm_id in ('u1337', 'u43110')

returns

"SRR10873916"	"u43110"	100	2.97e-66	"LAVDWTEFDSSQNNLEHALLRTVLGKLGAPLDVLDIIDQMKHTRYVENINVAGTVHSKKDSGAPDTLVGNTLFNLCVVLSCVDNYRQLEIAAFKGDDAIL"
"SRR10875094"	"u43110"	100	3.78e-66	"LAVDWTEFDSSQNNLEHALLRTVLGKLGAPLDVLDIIDQMKHTRYVENINVAGTVHSKKDSGAPDTLVGNTLFNLCVVLSCVDNYRQLEIAAFKGDDAIL"
"SRR10873446"	"u43110"	100	3.56e-66	"LAVDWTEFDSSQNNLEHALLRTVLGKLGAPLDVLDIIDQMKHTRYVENINVAGTVHSKKDSGAPDTLVGNTLFNLCVVLSCVDNYRQLEIAAFKGDDAIL"
"SRR8735790"	"u1337"	100	9.47e-71	"FSYDTRCFDSTVTEKDIRTEEEVYQCCDLEPEARKVIAALTERLYVGGPMHNSKGDLCGYRRCRASGVYTTSFGNTLTCYLKATAAIKAAGLRDCTMLVCGDDLVV"
"SRR10873776"	"u43110"	100	3.58e-65	"LAVDWTEFDSSQNNLEHALLRTVLGKLGAPLDVLDIIDQMKHTRYVENINVAGTVHSKKDSGAPDTLVGNTLFNLCVVLSCVDNYRQLEIAAFKGDDAIL"

So the interface should be able to "search" for one or more palm_id accessions. These would be "tags" which can be selected and added together. The graph should be updated to show the frequency count of matching libraries (ignore score for now, but ultimately score should be drawn as -log(evalue))

When the search is run, it should retrieve in the right panel the matching libraries which were build up in the query editor (left panel).