Question: search for class of proteins in unannotated genome
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gravatar for rob234king
4.5 years ago by
rob234king600
UK/Harpenden/Rothamsted Research
rob234king600 wrote:

I would like to search an unannotated genome for all amino acid transporters (pfam:PF01490). Whats the most effective way of doing this, blast sounds easy but the proteins are multi exon, I was thinking using hmm's but not sure how and if best option given searching genome. Can anyone recommend and maybe example linux commands etc.

blast • 906 views
ADD COMMENTlink modified 4.5 years ago by Asaf8.4k • written 4.5 years ago by rob234king600
0
gravatar for Asaf
4.5 years ago by
Asaf8.4k
Israel
Asaf8.4k wrote:

You can use tblastn and search the proteins in your database against the genome. If you want to scan peptides using HMM you can use interproscan.sh from http://www.ebi.ac.uk/interpro/download.html You can configure it to search only protein families from Pfam to narrow down the search. You'll have to find ORFs before you do this or predict genes (which is harder), ORFs can be found with EMBOSS getorf.

ADD COMMENTlink written 4.5 years ago by Asaf8.4k
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