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.