several MAFs

[Luana Arch]

Dear members,

I'm using mugsy to align 40 genomes, the output is a MAF file for each genome. Please can you point me to the part of the tutorial where I can read about extracting a given region from across all the files?

Best regards,

Anyela

[Robert Fitak]

I am not sure how you can have a separate alignment file for each genome?  Unless it is a diploid and you are aligning each chromosome for each genome?

Using MUGSY, you should get a single output file in MAF format, with all 40 genomes (sequences) in that alignment.  Each alignment block should have between 2-40 lines that begin with 's'.  With this alignment, you should easily be able to use the "ExtractFeature" function in MAFFILTER along with a gff file of intervals to isolate the regions of interest.