Free molecular biology software?

April 5, 2012 10:05 AM

I'm looking for good free software tools for doing basic molecular biology work - sequence alignments, DNA-protein translation, restriction mapping, and PCR primer design. Got any recommendations?

The last time I did this kind of work, six years ago, I used Vector NTI, but I don't need to do so much work this time, so I'd like to find something free.

posted by pombe to science & nature (8 answers total)

I don't do anything fancy, but I think ApE does a pretty good job and is easy to learn.
posted by juliapangolin at 10:17 AM on April 5, 2012

http://en.wikipedia.org/wiki/List_of_open_source_bioinformatics_software
posted by Blazecock Pileon at 10:25 AM on April 5, 2012

For de novo short read assemblers I've had some success with ABySS, SOAPdenovo and MIRA. Velvet seems popular though I've not had much luck with it.

For sequence alignment against a reference I use SMALT (full disclosure - I sit next to the programmer at work). The venerable cross_match is still good for capillary alignment. It's only free to academics though.
posted by antiwiggle at 10:38 AM on April 5, 2012

I'd recommend looking into what is available on the Galaxy system which has a nifty web interface.
posted by grouse at 10:56 AM on April 5, 2012

Yeah, ApE is all right. For primer design I usually use Primer3.

(I really wish there were a good open-source replacement for Vector NTI, especially now that it costs a million bajillion dollars per license.)
posted by en forme de poire at 11:08 AM on April 5, 2012

Here are the statistical genetics and phylogenetics pages with lots of packages for free statistical software R.
posted by shothotbot at 11:12 AM on April 5, 2012

I currently prefer Serial Cloner to ApE for basic cloning stuff (restriction mapping, construct design, in silico pcr and digests and ligations and whatnot.) I feel like ApE is a little more focused on sequence analysis, while Serial Cloner can handle stuff like Gateway-based cloning, shRNA production, and some other random things.

I'm assuming that by "sequence alignments" you mean "compare the sequencing results I got to the construct that I was trying to make and see if the cloning went well" rather than more involved genome/transcriptome alignment stuff, since VectorNTI is really for the former, not the latter. For that, there are a zillion implementations of ClustalX/other multiple sequence alignment tools; I usually use the online EBI ones when I just want to quickly check things. (EBI has a lot of basic tools you may find helpful.)

For primer design, I use Primer3 Plus, a slightly more user-friendly Primer3 web interface.
posted by ubersturm at 11:25 AM on April 5, 2012

Looks like ApE or Serial Cloner should do what I need, plus one or two other tools.

Thanks all!
posted by pombe at 11:59 AM on April 5, 2012