[Seqan-dev] about the best local alignment using BandedSmithWaterman

[Beifang Niu <neilniu.cn@gmail.com>]

Hi Seqan,

There is one function "localAlignment" in the Seqan tutorial.

Are there only three tags " BandedWatermanEggert, SmithWaterman, WatermanEggert" ?  I am wondering why there is no BandedSmithWaterman tag?

If I want to computes the best local alignment of two sequences using banded smithWaterman algorithm with fixed band length (for example: band length = 10 ),  Can I use LocalAlignment function to do that?

I have another question about the alignments and seed extension in the Seqan library.  It seems that there is no any parameter or return value for alignment identity ( matched base/ alignment length ) and the sequence identity of seed extension part (matched base / extension part length ).

Although, users can parse the alignment results or rewrite the seed extension code to get the sequence identity,  I still hope I can get sequence identity directly from alignments or seed extension results.

thanks,

Beifang