Blastall or blast+ (conversion tool?)

Question

[jomaco]

Following on from AHRD functional annotation program (error), the functional annotation program AHRD appears to require the results from blastp searches of proteins to various databases (sprot, trembl etc.) to be in blastall pairwise format instead of blast+ pairwise format.

Does it make a difference whether I use blastall or blast+? It seems the use of blast+ is recommended by NCBI - would the results be better using blast+?

Is there a script already available which can convert blast+ pairwise format files to blastall pairwise format files? (I have lots of blast+ generated files which I would like to use if possible).

Thanks

[5heikki]

Blast+ outputs 11 different formats + unlimited number of custom formats. Which particular format are you referring to? BLAST archive format (ASN.1)?

[jomaco]

Hi, I am referring to the "pairwise" output format (output format zero) which appears to be slightly different between blast+ blastp (2.2.29+) and blastall blastp (2.2.18)

Answer 1

[pld]

As far as I know they didn't change the pairwise output format, but I could be wrong. At least if they did change it, the BLAST team doesn't seem to have documented it.

From the module in BioJava that is throwing the exception, it seems that an outdated version of BioJava will throw this exception when it encounters a version of BLAST it isn't sure about.

http://www.biojava.org/pipermail/biojava-l/2003-January/003427.html

You may want to see if you can update your version of BioJava, or if you're feeling brave you can set a lazy mode that won't throw an exception if BioJava can't tell which BLAST version you're using.

I'm sorta confused as to why AHRD would want to use the text pairwise output as your desired input format. XML, tabular and so on are much easier to read and much less sensitive to small changes that could show up between BLAST versions.