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How to not get an overcounting of proteins sequences in database ?

I downloaded fasta files of proteins from Uniprot's database : ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Bacteria/

When i count number of proteins sequences of each file, i get an overcounting of proteins (isoforms), Is there a solution to exclude proteins isoforms ?

Thanks.

protein uniprot fasta
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updated by Elisabeth Gasteiger Elisabeth Gasteiger • written by yayuciara • yayuciara

1 answer

Have you read the README file in the top-level directory? ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/README

In the reference_proteome directory, we have attempted to automatically split all reference proteomes into 2 sets, the so-called "canonical" sequences ("one entry per gene") and "additional" sequences. Since this gene-centric procedure is fully automatic, the term "canonical" is used slightly differently than in the context of manual curation.

Do you have examples of organisms where you observe significant discrepancies?

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written by Elisabeth Gasteiger Elisabeth Gasteiger

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