Question: Command-line equivalent of online BLAST Needleman-Wunsch Global Alignment interface
gravatar for James Denvir
3.9 years ago by
James Denvir90
Marshall University, Huntington WV, USA
James Denvir90 wrote:

I was slightly surprised to find the online version of BLAST has an interface for global (Needleman-Wunsch) alignment.

Is there an equivalent command-line interface for this in the standalone version of BLAST? As far as I can tell from blastn -help, the command line version only runs local alignment.

blast • 2.7k views
ADD COMMENTlink written 3.9 years ago by James Denvir90

Even though it is available under the general tool heading of blast NCBI may be using a standard N-W implementation for global alignments. You could email blast support ( and confirm.

If you need a command line equivalent to use now then Needle from EMBOSS should work.

ADD REPLYlink written 3.9 years ago by GenoMax95k

Thanks for the comment. I was aware of Needle, but I've been using the command line version of blast and was just wondering if I could get away without another software dependency... The help for N-W on the online version I linked mentions the algorithm employs memory-use optimizations - which makes it sound like there may be some implementations that are non-standard in some sense. The link describing those is broken, which suggests this interface isn't in wide use, so probably Needle is the way to go.

ADD REPLYlink written 3.9 years ago by James Denvir90
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