<p>I&#39;m looking for a quick ftp-based solution to downloading FASTA canonical and splicing variants data from Uniprot:</p>

<p>Go to uniprot.org, type in Homo sapiens, click Download, select the format &quot;FASTA (canonical &amp; isoform)&quot;, click Go.</p>

<p>Can I automate this process for all organisms in the Uniprot database using ftp in one nice command line utility?</p>

<p>You can download precomputed reference proteomes by ftp. They include canonical and fasta sequences:</p>

<p>ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/reference_proteomes/</p>

<p>( see also http://www.uniprot.org/help/reference_proteome )</p>

<p>If this is not what you want, you can indeed automate the http download, as described in the <a href="http://www.uniprot.org/help/programmatic_access">UniProt help page for programmatic access</a>, in particular <a href="http://www.uniprot.org/help/programmatic_access#retrieving_entries_via_queries">Retrieving entries via queries</a></p>

<p>e.g. http://www.uniprot.org/uniprot/?query=organism:9606&amp;format=fasta&amp;include=yes&amp;compress=yes</p>

<p>Please note that large http downloads are much more vulnerable and likely to fail than ftp downloads.</p>

<p>Please don&#39;t hesitate to contact the UniProt helpdesk if you have any additional questions.</p>
