Sequence Database Setup: SwissProt

SwissProt Release 56.0 The syntax of the Fasta title line changed (again!) in SwissProt release 56.0 (UniProtKB 14.0). This page has been updated to illustrate the new parse rules.

Overview

The database is developed by the SWISS-PROT groups at SIB and EBI.

Download

The EBI site mirrors the Expasy site. The files are:

• Version info: reldate.txt
• Fasta file: uniprot_sprot.fasta.gz
• Dat file: uniprot_sprot.dat.gz

To download updates automatically, the relevant definition blocks in db_update.pl is SwissProt_complete_from_EBI. There is also a definition for downloading just the SwissProt Fasta file: SwissProt_fasta_only_from_EBI.

Taxonomy

If you do not wish to have a local copy of the Dat file, and prefer to take taxonomy from the Fasta file instead, you will need to update the taxonomy definition in mascot.dat. Make a backup copy of mascot.dat, then use a text editor to change taxonomy block 3 as follows:

# TAXONOMY FOR SwissProt or Trembl from the fasta file
Taxonomy_3
Identifier SwissProt FASTA
Enabled 1 # 0 to disable it
FromRefFile 0
DescriptionLineSep 0 # ctrl a - hex code '1'. For multiple descriptions per entry
SpeciesFiles NCBI:names.dmp
NodesFiles NCBI:nodes.dmp
DefaultRule NCBI, CHOP:W "OS=\(.*\) PE=" # from release 14.0 onwards
end

Note that mascot.dat must be saved as plain text, so be careful if using a word processor, and ensure the filename is not changed to mascot.dat.txt or something.

Having made these changes, in database maintenance, choose "SwissProt FASTA".

The following taxonomy files are required:

ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/docs/speclist.txt

Note that the taxonomy files go into the taxonomy directory, not into the sequence database directory. Also, some files need to be unpacked (using tar) as well as uncompressed.

Parse Rules

>sp|Q4U9M9|104K_THEAN 104 kDa microneme/rhoptry antigen OS=Theileria annulata GN=TA08425 PE=3 SV=1

You can use either the ID (104K_THEAN) or the AC (Q4U9M9) as the identifier. Many people prefer the ID because it is semi-descriptive.

ID from Fasta title: ">..|[^|]*|\([^ ]*\)"
AC from Fasta title: ">..|\([^|]*\)"
Description from Fasta title: ">[^ ]* \(.*\)"

The corresponding line in the Dat file is:

ID   104K_THEAN              Reviewed;         893 AA.

ID from Ref file: "^ID   \([^ ]*\)"

Configuration

When updating an active database, it is important to rename the Fasta file last, because Mascot will begin database exchange as soon as it sees a new Fasta file that matches the wildcard path for the database.

If you decide not to have the reference file locally, full text for individual entries can be retrieved across the web from an SRS server or Expasy. This can be done using either the ID or the AC as the identifier. For Expasy, the syntax for the Path field is:

/cgi-bin/get-sprot-raw.pl?#ACCESSION#

Where #ACCESSION# represents either the AC or ID. For an SRS server, the syntax for the Path field is:

Retrieve by ID: /srsbin/cgi-bin/wgetz?-e+[SWISSPROT-id:#ACCESSION#]+-vn+2
Retrieve by AC: /srsbin/cgi-bin/wgetz?-e+[SWISSPROT-acc:#ACCESSION#]+-vn+2

This screen shot illustrates a configuration in which the identifier is AC and there is no local Dat file:

Make sure that the final parse rule has the correct case. Early versions of wgetz return HTML pages tagged with <PRE>, while later versions use <pre>. Parse rules are always case sensitive.

If you don't require full text in a Mascot Protein View report, simply leave the Host, Port, and Path fields blank and choose
--- no full text report ---
in the drop down list.

Always test a new definition before applying the changes to mascot.dat.