Difference Between Blastall And Blastn?

Question

[2184687-1231-83-]

What is the difference, other than subtle different in the output format, between "blastall -p blastn" and running NCBI-Blast+ blastn?

Are the results supposed to be the same in terms of sensitivity/specificity?

[Ketil]

I think they're the same program - blastn is the newer BLAST+ package, blastall -p blastn is from the old NCBI BLAST.

[Michael Schubert]

NCBI is shifting from C to C++, hence the + in the name (same with the toolbox).

Answer 1

[Michael Kuhn]

This is what the NCBI says about the difference between BLAST and BLAST+:

The BLAST+ applications have a number of performance and feature improvements over the legacy BLAST applications. For details, please see the BLAST+ user manual and the article in BMC Bioinformatics (PubMed link).

So I guess the main differences are in performance, but it might also be that BLAST+ uses better default settings that are kept unchanged in BLAST for reasons of backwards compatibility.

[Michael Kuhn]

If you do any kind of parsing, the tabular and XML output formats are probably much better suited.

[2184687-1231-83-]

I am annoyed by the fact that the output format has subtly changed between one and the other, but clearly they are different beasts altogether, thx.

Answer 2

[Ed]

Hi,

I have run the blastn option in blastall with the following command:

blastall -p blastn -i query.fa -d subject -e 0.00001 -v 1 -b 1 -o blastn.blastn -a 14

and blastn in the BLAST+ package with:

blastn -task blastn -query query.fa -db subject -evalue 0.00001 -num_descriptions 1 -num_alignments 1 -out blastn.blastn -num_threads 14

using the same query and subject data. I have obtained more hits using the BLAST+ blastn, and these hits also had higher bit scores and much lower E values.

Just wondering if others have had the same experience, and whether this could be because the underlying algorithm/default parameters of blastn are different between the blastall and BLAST+ versions.

Cheers,

Ed