I'd like to use graph aligner to realign or patch up partial alignments in GAF format. The alignment will have some unaligned regions, and I'd like to obtain an alignment of the query across these incomplete portions.
Is this close enough to the way that MEM chains are aligned that it would be easy to implement? Where would you suggest to start?
I'd like to use graph aligner to realign or patch up partial alignments in GAF format. The alignment will have some unaligned regions, and I'd like to obtain an alignment of the query across these incomplete portions.
Is this close enough to the way that MEM chains are aligned that it would be easy to implement? Where would you suggest to start?