any tool for searching duplicated or redundant sequences in a database?

Question

[v.berriosfarias]

Hello I'm building a prokaryotic protein database and I have used different sources of sequence databases, its likely the fact that on my new database more than 1 repeated sequence is present. Is there any tool for estimating sequence similarity on a single fasta file (my database)?

Thank for your time

[Pierre Lindenbaum]

How can I BLAST each sequence in a FASTA-file against all the other sequences in the same file? ?

Answer 1

[GenoMax]

cd-hit (LINK) or MMseq2 cluster (LINK) can both help generate non-redundant sequences. In fact NCBI is now using mmseq2 to cluster nr for their web version.

Answer 2

[Hugo]

You can use SEDA (https://www.sing-group.org/seda/). The "Remove Redundant Sequences" operation (https://www.sing-group.org/seda/manual/operations.html#remove-redundant-sequences) allows to do this.