July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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megablast Parameters
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-S [1..2]
Default: 1
The strand on subsequence. Only used with nucleotide sequences.
1 Top strand
2 Bottom strand
-t [T/F]
Default: F
The definition line should contain target GI only. This parameter applies only to nonredun-
dant databases. When set, only the definition line corresponding to the GI is reported, not
the redundant definition lines. No such mechanism exists for accession numbers; redun-
dancies are always reported.
-T [T/F]
Default: F
Gets taxonomy information from an NCBI-formatted BLAST database. The downloadable
FASTA files don’t allow this feature; only the preformatted will work. The preformatted
databases can be found at ftp://ftp.ncbi.nlm.nih.gov/blast/db/FormattedDatabases/.
megablast Parameters
megablast is similar to blastn but optimized to find near identities very quickly. It’s
much faster than the standard blastn, partly because it uses query packing. The
extension algorithm differs from the standard blastn and isn’t designed for cross-spe-
cies searches. Many parameters are identical between megablast and blastall, but
some are unique to one program or the other, and some parameters with the same
symbol do different things.
Here are a few example command lines:
megablast -d my_db -i my_query -F "m D"
megablast -d my_db -i my_query -D 2 -t 18 ...
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O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.Julian F.
I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.