Question: Easier way to filter contaminants based on protein similarity ?
0
gravatar for Biogeek
3.7 years ago by
Biogeek400
Biogeek400 wrote:

Hey guys,

I'm familiar with the idea of blob plots, but for filtering off contaminants in a plant I've sequenced. I've so far used a manual screening protocol, whereby I take the top hit of each query ( sim identity , but score and e value) . I then use the uniprot and trembl species identifiers to filter off plausible contaminants such as bacteria etc.

Doing this takes a hellish long time in excel, manually. Is there anyway I can filter off all hits which are not in green plants? I am using the entire uniprot and trembl as the plant I'm working on commonly has lots of bacteria and fungi on it. I have the uniprot/ trembl identifier available to me.

Any help appreciated.

uniprot diamond blastx trembl • 974 views
ADD COMMENTlink modified 3.7 years ago by Elisabeth Gasteiger1.7k • written 3.7 years ago by Biogeek400
0
gravatar for Elisabeth Gasteiger
3.7 years ago by
Geneva
Elisabeth Gasteiger1.7k wrote:

Have you tried to perform your BLAST searches against the Plants subsection of UniProtKB in the first place? e.g. on the UniProt website http://www.uniprot.org/blast, or programmatically using one of

ADD COMMENTlink written 3.7 years ago by Elisabeth Gasteiger1.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1335 users visited in the last hour