BLAT standalone or any other tool to map/extract gene sequences from genomic sequence using CDS as queries

Question

[imaditi1987]

Hi!!

I need to get all the gene sequences from the genomic sequence based on file of CDS sequences as a query.

I tried using BLAST which was a bad choice. I read somewhere that BLAT and GMAP would be the ideal programs to do this..Suggest me if BLAT or GMAP or any other software is available for windows to do this task. I'm a windows user with some preliminary knowledge of python.

Answer 1

[Michael]

gmap and exonerate with option --model est2genome should do that.

Answer 2

[imaditi1987]

Thanks for the reply.

Are both these softwares available for windows. Can you tell me bit about installing exonerate.

[thackl]

exonerate is very good in aligning EST/CDS/transcripts, but it is also very slow if you use it for entire genomes - it is not a mapper. There is a comprehensive beginners guide here. Both, exonerate and gmap, can by run on Windows via cygwin.