BLAST Global alignment

Question

[James Sacco]

Hi all, I want to know if there is a way to run the BLAST Specialized search called Global Align from the (UNIX) command line. (I'm working on an Ubuntu distro.)

I cannot find any mention of Global Align in the BLAST+ user manual, and on the web it appears to be nested as a special tool under BLASTn.

Background: I have a batch of DNA sequences I want to globally align with a query DNA sequence, but I do not want to run each one individually against the query. I would like to loop/iterate through those subject sequences, and output a text or csv file with metrics about their gaps, mismatches, % identity, etc. If you know of a different tool that can do this, please let me know. I know about EMBOSS Needle, but do not know if that is also available from the command line.

tl;dr: I need a global alignment tool that can process a list of sequences against one query sequence, and a way to save that output as text or csv.

Thanks!

Answer 1

[GenoMax]

EMBOSS (LINK) is available for download as a command line package.

BLAST as the name suggests is a local alignment program. Where do you see "Global Align" on web blast? Perhaps you are referring to blast two sequences against each other option or Needleman-Wunsch global alignment pages?

EMBOSS suite has a blast2seq tool available in addition to needle. Other tools like MUMmer4 (LINK) may also be useful.

[James Sacco]

Thanks for the helpful links,@GenoMax. NCBI Global Align does Needleman-Wunsch, and it's at the bottom of the BLAST page (under Specialized Searches). That is the alignment I wanted, but I just wanted to automate the process so it loops over my list of short sequences, instead of having to input and save the stats one-by-one. I think the tools you referenced will do the job. Thanks again!