Question: tblastn extend beyond homology region
0
gravatar for Amaranta_Remedios
8 months ago by
The university of Manchester, UK
Amaranta_Remedios0 wrote:

Hi,

I am performing a very simple task. I got a protein sequence, with conserved domains and I am mapping this protein and domains to a genome. I found the analogous domain. However I would like to get 100 amino acids downstream and upstream the domain. Because its a tblastn I am a bit stuck on how to do that properly to get everything on the same reading frame.

Any suggestion?

Thanks !

blast • 124 views
ADD COMMENTlink modified 8 months ago by maxime.policarpo110 • written 8 months ago by Amaranta_Remedios0
0
gravatar for maxime.policarpo
8 months ago by
France, Paris
maxime.policarpo110 wrote:

Are you trying to find the orthologous sequence from your protein in a genome ? If so, you can just extract your tblastn region with samtools faidx (like 100000bp upstream + 100000bp downstream) and then use exonerate to find the CDS of your gene on this genome, which will give you the exon sequences and also the intron borders.

ADD COMMENTlink written 8 months ago by maxime.policarpo110
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