Question: Extracting fasta sequence from CDS matching with sequence ID
gravatar for metallicasster
8 weeks ago by
metallicasster0 wrote:

I am trying to extract matching sequences from a header list file. My fasta sequence looks like this :

>TRINITY_DN0_c0_g1_i1.p1 TRINITY_DN0_c0_g1~~TRINITY_DN0_c0_g1_i1.p1  ORF type:complete len:141 (-),score=18.99,CCNL1_PONAB|68.750|6.95e-55,Cyclin_N|PF00134.23|6.5e-09 TRINITY_DN0_c0_g1_i1:85-507(-) 

ATG <sequences in between>................TAG

I have a separate header file <header.list> that that has list of headers like TRINITY_DN0_c0_g1_i1

I now want to extract fasta file along with header that matches my header file.

The problem that i have is : those fasta headers are long enough and does not match with my header.list ( as these headers are just a part of headers in fasta file).

Does anyone have any idea how to overcome this problem

sequence gene • 99 views
ADD COMMENTlink modified 8 weeks ago by RamRS28k • written 8 weeks ago by metallicasster0

This question has been answered multiple times on the forum. Please search the forum for "fasta extract id"

ADD REPLYlink written 8 weeks ago by RamRS28k
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