MAF sequence names about cactus

[glennhickey]

the only names attached to sequences are the species.chromosome i.e., Mus_musculus.NC_000072.7

What more do you want?

[austinchipps]

Hey Glenn,

Apologies if my original question wasn't clear. So in my MAF file I have multiple aligned regions (genes in this case) from the same chromosome. So alignments of 'gene1' and of 'gene2' are going to have the same name if they come from the same chromosome. Chromosome name in my example above is "Mus_musculus.NC_000072.7". Since I have a BED file of target genes including their names in addition to the coordinates, I was wondering if ya'll had a tool or recommended way to distinguish alignments of different genes from the same chromosome. My goal is to eventually split the alignment (after converting to fasta) so I end up having one alignment file for each aligned gene. I haven't been able to accomplish this yet because the names of what's aligned are repetitive.

Austin