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

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
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updated by Biostar Biostar • written by kanshenglong • kanshenglong

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

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written by kanshenglong • kanshenglong

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

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written by Sej Modha Sej Modha

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.

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written by GenoMax GenoMax

Use bwa mem -Y....

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written by lh3 lh3

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