Extracting fasta sequence from CDS matching with sequence ID

0

Entering edit mode

3.9 years ago

metallicasster • 0

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 • 662 views

ADD COMMENT • link updated 3.9 years ago by Ram 43k • written 3.9 years ago by metallicasster • 0

1

Entering edit mode

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

ADD REPLY • link 3.9 years ago by Ram 43k

Login before adding your answer.