Question: extract gene from MCL out
0
gravatar for akhilvbioinfo
2.8 years ago by
akhilvbioinfo130
India, chennai
akhilvbioinfo130 wrote:

Hai there

I want to find HGC (Homologous Gene clustering) of a species . I started with BLAT to align genes of my species against each other. MCL software (Markov Clustering Algorithm) was used to create HGSc from BLAT alignment. I got an file "fname-out" from MCL. I want to extract gene sequence of each cluster .Is there any software or programme for this?

mcl gene • 795 views
ADD COMMENTlink written 2.8 years ago by akhilvbioinfo130

head fname-out should give you an idea of what the file contains. You could have identifiers as clusters in the file, with which you can query a gene database in NCBI or EMBL and extract sequences with a simple script.

Until you peek into the file, your next steps can not be easily determined by others.

ADD REPLYlink written 2.8 years ago by RamRS21k
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: 1118 users visited in the last hour