Question: Multiple Sequence Alignment In C
0
gravatar for Isaac Turner
7.5 years ago by
Isaac Turner50
United Kingdom
Isaac Turner50 wrote:

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 • 2.9k views
ADD COMMENTlink modified 6.7 years ago by Biostar ♦♦ 20 • written 7.5 years ago by Isaac Turner50
3

I think seqan must have this functionality.

ADD REPLYlink written 7.5 years ago by lh332k

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

ADD REPLYlink written 7.5 years ago by Isaac Turner50

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

ADD REPLYlink written 7.5 years ago by ewre220
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