11-18-2010
Quote:
Originally Posted by
pludi
It's pretty much useless on Linux, since almost all current distributions allow you to automatically update the system to the latest security patches, including all applications and plugins installed through the package manager.
Thanks for the reply...
Thats my initial thought too, like you said. But what about applications that aren't installed through the package manager, like Adobe Flash? I installed it through Firefox, but maybe it uses the package manager too?
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LEARN ABOUT DEBIAN
psi-cd-hit
PSI-CD-HIT.PL(1) User Commands PSI-CD-HIT.PL(1)
NAME
psi-cd-hit.pl - runs similar algorithm like CD-HIT but using BLAST to calculate similarities
DESCRIPTION
Usage psi-cd-hit [Options]
Options
-i in_dbname, required
-o out_dbname, required
-c clustering threshold (sequence identity), default 0.3
-ce clustering threshold (blast expect), default -1,
it means by default it doesn't use expect threshold, but with positive value, the program cluster seqs if similarities meet either
identity threshold or expect threshold
-L coverage of shorter sequence ( aligned / full), default 0.0
-M coverage of longer sequence ( aligned / full), default 0.0
-R (1/0) use psi-blast profile? default 0 perform psi-blast / pdb-blast type search
-G (1/0) use global identity? default 1 sequence identity calculated as
total identical residues of local alignments / length of shorter seq
if you prefer to use -G 0, it is suggested that you also use -L, such as -L 0.8, to prevent very short matches.
-d length of description line in the .clstr file, default 30 if set to 0, it takes the fasta defline and stops at first space
-l length_of_throw_away_sequences, default 10
-p profile search para, default
"-a 2 -d nr80 -j 3 -F F -e 0.001 -b 500 -v 500"
-bfdb profile database, default nr80
-s blast search para, default
"-F F -e 0.000001 -b 100000 -v 100000"
-be blast expect cutoff, default 0.000001
-b filename of list of hosts to run this program in parallel with ssh calls, you need provide a list of hosts
-pbs No of jobs to send each time by PBS querying system
you can not use both ssh and pbs at same time
-k (1/0) keep blast raw output file, default 1
-rs steps of save restart file and clustering output, default 5000
everytime after process 5000 sequences, program write a restart file and current clustering information
-restart restart file, readin a restart file
if program crash, stoped, termitated, you can restart it by add a option "-restart sth.restart"
-rf steps of re format blast database, default 200,000
if program clustered 200,000 seqs, it remove them from seq pool, and re format blast db to save time
-local dir of local blast db,
when run in parallel with ssh (not pbs), I can copy blast dbs to local drives on each node to save blast db reading time BUT, IT MAY
NOT FASTER
-J job, job_file, exe specific jobs like parse blast outonly DON'T use it, it is only used by this program itself
-single files of ids those you known that they are singletons
so I won't run them as queries
============================== by Weizhong Li, liwz@sdsc.edu ==============================
If you find cd-hit useful, please kindly cite:
"Clustering of highly homologous sequences to reduce thesize of large protein database", Weizhong Li, Lukasz Jaroszewski & Adam
GodzikBioinformatics, (2001) 17:282-283 "Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide
sequences", Weizhong Li & Adam Godzik Bioinformatics, (2006) 22:1658-1659
psi-cd-hit.pl 4.6-2012-04-25 April 2012 PSI-CD-HIT.PL(1)