Some people in my lab use megablast from BLAST 2.2.20 claiming that it is magically faster than the latest.
So I went to search for it to see what the difference is:
...Deep in the dungeons of NCBI
> ftp> ls
229 Entering Extended Passive Mode (|||50259|)
150 Opening ASCII mode data connection for file list
dr-xr-xr-x 2 ftp anonymous 4096 Nov 20 2008 2.2.18
dr-xr-xr-x 2 ftp anonymous 4096 Jul 22 2009 2.2.19
dr-xr-xr-x 2 ftp anonymous 4096 Jul 27 2009 2.2.21
dr-xr-xr-x 2 ftp anonymous 4096 Oct 14 2009 2.2.22
dr-xr-xr-x 2 ftp anonymous 4096 Mar 22 2010 2.2.23
dr-xr-xr-x 2 ftp anonymous 4096 Nov 12 16:17 2.2.24
lr--r--r-- 1 ftp anonymous 6 Aug 23 2010 LATEST -> 2.2.24
What?! Where is 2.2.20?
Did the magi of NCBI retract it from their FTP for simply being too fast for the database queries of man?
Do any NCBI historians know what happened?
•
written
by
Science_Robot
You were most likely looking in the ftp.ncbi.nih.gov/blast/executables/blast+ directory. According to the release notes, 2.2.21 was the first to ship the BLAST+ command-line tools (the older versions of BLAST+ were most likely not fully ported to C++ at the date of the release).
2.2.20 can be found the in the C-tree of the releases. Since you mentioned megablast, the version your people are using definitely belongs there.
Note that there was a discussion on Biostar whether BLAST or BLAST+ was faster that came to the opposite conclusion.
•
written
by
Michael Schubert
But versions 2.2.19 and 2.2.18 are still there.
Also, I'm talking about the megablast executable for blastn. I think the difference might just be a result of default word-length.
Also, 2.2.20 uses all cores regardless of whether or not the subject database is split up.
Well, see if your people are actually using 2.2.20 or 2.2.20+. If it's the first one, NCBI will not have released 20+ for some reason. If it's the latter and NCBI did take down the release again, I suggest they had a good reason to and you don't use it.
Well, see if your people are actually using 2.2.20 or 2.2.20+. If it's the first one, NCBI will not have released 20+ for some reason. If it's the latter and NCBI did take down the release again, they probably had a good reason to and I suggest you don't use it.
Are the C and C++ versions being developed in parallel? I noticed that there is a version 2.2.25 for the C version.
Log in to answer this question.
