CD-HIT-2D

Reference

CD-HIT-2D compares 2 protein datasets (db1, db2). It identifies the sequences in db2 that are similar to db1 at a certain threshold. The input are two protein datasets (db1, db2) in fasta format and the output are two files: a fasta file of proteins in db2 that are not similar to db1 and a text file that lists similar sequences between db1 & db2.

Category

Sequence Analysis

Usage

cd-hit-2d -i db1 -i2 db2 -o db2novel -c 0.9 -n 5

Manual

where
db1 & db2 are inputs,
db2novel is output,
0.9 means 90% identity, is the comparing threshold
5 is the size of word

Options, -b, -M, -l, -d, -t, -s, -S, -B, -p, -aL, -AL, -aS, -AS, -g, -G, -T are same to CD-HIT, here are few more cd-hit-2d specific options:

-i2 input filename for db2 in fasta format, required
-s2 length difference cutoff for db1, default 1.0
    by default, seqs in db1 >= seqs in db2 in a same cluster
    if set to 0.9, seqs in db1 may just >= 90% seqs in db2
-S2 length difference cutoff, default 0
    by default, seqs in db1 >= seqs in db2 in a same cluster
    if set to 60, seqs in db2 may 60aa longer than seqs in db1

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