local alignment with a sets of sequences in a fasta file to a reference sequence.

Question

[kanshenglong]

I am in need of some help again.

I have a set of sequences (in a multifasta file), and I need to align them against a reference with local alinment. I have tried EMBL-EBI pairwise alignment tools, but it just calculate the local alignment of two sequences. And 'bwa mem' does a local alignment, it only aligns the best matching parts of my contigs while the remainder is clipped off, but I need the intact sequences. Other software that can be useful?

Thanks in advance.

[lh3]

Use bwa mem -Y....

[kanshenglong]

Can I retrieve such alignment in a fasta format? Thanks a lot.

[Sej Modha]

I have not tried it before but bwasw option of bwa might work.

[GenoMax]

Look at the pair-wise alignment output formats from EMBOSS on this page (markxN series). I assume you are referring to EMBOSS tools on the EBI site. It may be that you just need to select -aformat markx0 as output for your pairwise alignment.