extract gene from MCL out

Question

[Eva_Maria]

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?

[Ram]

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.