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

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7.7 years ago

kanshenglong • 0

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.

alignment • 2.3k views

ADD COMMENT • link updated 7.6 years ago by Biostar 20 • written 7.7 years ago by kanshenglong • 0

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Use bwa mem -Y....

ADD REPLY • link 7.7 years ago by lh3 33k

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

ADD REPLY • link 7.7 years ago by kanshenglong • 0

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

ADD REPLY • link 7.7 years ago by Sej Modha 5.3k

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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.

ADD REPLY • link 7.7 years ago by GenoMax 141k

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