Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups Of Redundant Acc Numbers*

Question

[angel.roey]

Is there a way to remove redundant amino acid sequences from a fasta file but also output all the redundant accession numbers in groups, just like mothur's unique.seqs command (which unfortunately only works on nucleic acids data). the accession number output should look like this (or similar):

G9SS7BA01AM9A3    G9SS7BA01AM9A3,G9SS7BA01EMTMV,G9SS7BA01CYG40,G9SS7BA01AWI8Z,G9SS7BA01AFVJC,G9SS7BA01BCZCD,G9SS7BA01DBN7B,G9SS7BA01CZ7GO,G9SS7BA01C05FB
G9SS7BA01EAKDX    G9SS7BA01EAKDX,G9SS7BA01B1MNY
G9SS7BA01C2SRQ    G9SS7BA01C2SRQ,G9SS7BA01AK1UJ,G9SS7BA01BLVCZ,G9SS7BA01ARMFA
G9SS7BA01BQ5UG    G9SS7BA01BQ5UG,G9SS7BA01BZ9XF
G9SS7BA01BD4F9    G9SS7BA01BD4F9

Where each row is a group of identical seqs and the first column is the one kept in the 'uniques' file.

USEARCH only outputs a file with the unique seqs.

Answer 1

[Damian Kao]

You can use CD-HIT (http://weizhong-lab.ucsd.edu/cd-hit/) and parse the resulting cluster file into tab delimited format.

The only problem you might face with CD-HIT is that if your sequence IDs are really long, the cluster output file will shorten the name automatically. You might have rename your fasta files first to a shorter name and then remap the names back afterwards.

[cts]

You can change the maximum allowed length of the description in the cd-hit output file with the -d option

[Damian Kao]

Nice. I didn't know that. I guess I should really go through the options.

[angel.roey]

Thanks! Any possibility of influencing what is being written to the CLSTR file? e.g. only include seqs with redundancy, change format etc.

[angel.roey]

Doesn't matter, USEARCH does all I need.

Answer 2

[cts]

From memory, Usearch should give you the cluster file if you provide it the -uc <FILENAME> option

[angel.roey]

Thanks! It does. And in a nicer format than cd-hit

Answer 3

[Eslam Samir]

Here is my free program on Github Sequence database curator (https://github.com/Eslam-Samir-Ragab/Sequence-database-curator)

It is a very fast program and it can deal with:

1. Nucleotide sequences
2. Protein sequences

It can work under Operating systems:

1. Windows
2. Mac
3. Linux

It also works for:

1. Fasta format
2. Fastq format

Best Regards