Multiple Sequence Alignment In C

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10.9 years ago

Isaac Turner ▴ 50

I want to do multiple sequence alignment in a program I'm writing in C, and will likely end up calling it millions of times with short DNA sequences (<10 sequences, <200bp). Do you know of any multiple sequence alignment libraries that provide an API that I can use? I could write the sequences to the file, make a system call to run a common alignment program (e.g. MUSCLE) then read in the results, but given the number of calls I'll be making this seems quite slow to do all the message passing on disk.

I'm ideally looking for a library in C/C++ with a simple API, with a GPL/MIT/BSD license. Does anyone have any experience of this?

multiple-alignment c • 3.7k views

ADD COMMENT • link updated 10.1 years ago by Biostar 20 • written 10.9 years ago by Isaac Turner ▴ 50

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I think seqan must have this functionality.

ADD REPLY • link 10.9 years ago by lh3 33k

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I wrote a small wrapper in C to call seqan and it seems to work great - thanks.

ADD REPLY • link 10.9 years ago by Isaac Turner ▴ 50

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as is recomended by lh3, seqan should be your choice, bowtie also use this library too.

ADD REPLY • link 10.9 years ago by ewre ▴ 250

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