Question: extract gene from MCL out
gravatar for akhilvbioinfo
4.2 years ago by
India, chennai
akhilvbioinfo150 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 • 1.0k views
ADD COMMENTlink written 4.2 years ago by akhilvbioinfo150

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 4.2 years ago by RamRS30k
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