[Biopython] traditional NCBI blast vs. blast+

[Paulo Nuin]

Hi 

Just answering your blast portion of the question:

- you have to run makeblastdb in order to create the database.
- you should be able to download the source of blast+ to compile, it should compile just fine on your system
- and yes, it seems to be faster and more stable than the previous version, at least on the tests I run

Paulo



On 2011-03-02, at 6:00 PM, Martin Mokrejs wrote:

> Hi,
>  I needed to run and parse some blastn analysis. I had a look into the Tutorial
> and followed the currently recommended blast+ approach. Somewhat I was not
> getting any results. It seems to me a formatdb-formatted database is not readable
> by the blast+ tools. I had a look what tools are installed on my Gentoo Linux
> along with blastn, blastx and the other tools coming from blast+ bundle and from
> filenames I just could not guess what am I supposed to run over my fasta
> target database to make it searchable by blastn. I would prefer if biopython
> would throw out some error if there are no appropriate files (which names could
> be guessed depending on the (t)blastn/x/p, etc.).
>  The tutorial mentions that I should lookup an older version of the Tutorial
> for examples on the old, NCBI blast usage via biopython. It took me a while but
> I found through Google some docs like that. ;-)
>  On Gentoo the ncbi-tools++ (aka blast+) package installs no documentation,
> not a single README, HOWTO, Changes, just the binaries and libs. What is installed
> on other Linux platform, would you mind sharing this with me? I just failed
> to find by Google what tools should I use instead of the formatdb. I found
> some FAQ on the NCBI tools++ site but that talked just about C++ API etc.,
> nothing from the user perspective.
>  On Gentoo, the {asn2asn,rpsblast,test_regexp} from ncbi-tools++ is not being
> installed because they have same name as the same utility from "old" ncbi-tools
> (hence overwting their files). The ncbi-tools++ package is not allowed to be
> installed on stable "systems" (lack of testing or open bug reports) so most people
> using Gentoo do NOT have ncbi-tools++ and probably won't for a while.
>  I propose to keep support for the "old" blast for a long while. Luckily, the
> blastall -m 7 xml output seems to be parseable with Bio.Blast.NCBIXML.
> 
>  What do you think? Is the blast+ approach faster, more stable, or just newer
> so we all like to "upgrade"? Where are some docs and what is the formatdb-like
> tool in blast+. ;)
> Thanks,
> Martin
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