Aligning UniProt Canonical Sequences With Their Isoform Sequences

Question

[pwg46]

Hello,

I notice that when I input a UniProt into UniProt's website, the result page has an "Alternative Sequence" section, which shows exactly how and where each of the UniProt's isoforms differ from the canonical sequence. I am unable to find this information in any of UniProt's ftp files. Could someone point me in the direction of a data file containing this information? I require it to align canonical sequences to their isoforms. The data must be somewhere, given that they display it in a section on their result page.

Answer 1

[Elisabeth Gasteiger]

Isoform sequences can be downloaded in FASTA format from our FTP download index page http://www.uniprot.org/downloads : choose the file: 'Isoform sequences'
(see also http://www.uniprot.org/help/canonical_and_isoforms).

The direct path to the FTP server is
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot_varsplic.fasta.gz