What it does
CD-HIT stands for Cluster Database at High Identity with Tolerance. The program (cd-hit) takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr) representative sequences as output. In addition cd-hit outputs a cluster file, documenting the sequence 'groupies' for each nr sequence representative. The idea is to reduce the overall size of the database without removing any sequence information by only removing 'redundant' (or highly similar) sequences. This is why the resulting database is called non-redundant (nr). Essentially, cd-hit produces a set of closely related protein families from a given fasta sequence database.
Inputs
cd-hit requires a protein fasta file as input.
Outputs
The first output is a fasta file containing representative sequences.
The second output is a text file listing the mapping of sequences to the representative sequences:
>Cluster 0 0 2799aa, >PF04998.6|RPOC2_CHLRE/275-3073... * >Cluster 1 0 2214aa, >PF06317.1|Q6Y625_9VIRU/1-2214... at 80% 1 2215aa, >PF06317.1|O09705_9VIRU/1-2215... at 84% 2 2217aa, >PF06317.1|Q6Y630_9VIRU/1-2217... * 3 2216aa, >PF06317.1|Q6GWS6_9VIRU/1-2216... at 84% 4 527aa, >PF06317.1|Q67E14_9VIRU/6-532... at 63% >Cluster 2 0 2202aa, >PF06317.1|Q6UY61_9VIRU/8-2209... at 60% 1 2208aa, >PF06317.1|Q6IVU4_JUNIN/1-2208... * 2 2207aa, >PF06317.1|Q6IVU0_MACHU/1-2207... at 73% 3 2208aa, >PF06317.1|RRPO_TACV/1-2208... at 69%