[Biopython] traditional NCBI blast vs. blast+

[Martin Mokrejs]

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