psi-cd-hit-2d (1)

Usage psi-cd-hit-2d [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 -i2 second input database -blastn run blastn, default 0 -lo how long can seq in db2 > db1 in a cluster, default 0

• means, that seq in db2 should <= seqs in db1 in a cluster

• ============================== by Weizhong Li, [email protected] ==============================

• 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