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?
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2184687-1231-83-
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.
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Michael Kuhn
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.
If you do any kind of parsing, the tabular and XML output formats are probably much better suited.
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
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I think they're the same program - blastn is the newer BLAST+ package, blastall -p blastn is from the old NCBI BLAST.
NCBI is shifting from C to C++, hence the + in the name (same with the toolbox).