PSI-CD-HIT

Reference

PSI-CD-HIT clusters proteins into clusters that meet a user-defined similarity threshold, which can be identity or expect value. Each cluster has one representative sequence. The input is a protein dataset in fasta format and the outputs are two files: a fasta file of representative sequences and a text file of list of clusters

Category

Sequence Analysis

Usage

psi-cd-hit.pl -i nr60 -o nr30 -c 0.3

Manual

Options, -l, -d, -s, -S are same to CD-HIT, here are few more psi-cd-hit specific options:

-ce clustering threshold (blast expect), default -1, by default it doesn't use
    expect threshold, but with positive value, the program cluster sequences if
    similarities meet either identity threshold or expect value threshold
-L  coverage of shorter sequence (aligned / full), default 0
-M  coverage of longer sequence (aligned / full), default 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 sequence
-be blast expect cutoff, default 0.000001
-b  filename of list of hosts, to run this program in parallel with ssh calls

Share your experience or ask a question