Mascot database search > Help > Sequence database setup > TrEMBL

Sequence database setup: TrEMBL

This is a Predefined Database Definition

Trembl is a predefined database, meaning up-to-date configuration information can be downloaded automatically by Mascot Database Manager. Choose Trembl_ID to use the ID as the unique identifier or choose Trembl_AC to use the AC. The configuration information on this page is maintained as a service to users of Mascot 2.3 and earlier.

Overview

UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization. About 85 % of the protein sequences in UniProtKB are derived from the translation of coding sequences (CDS) from the EMBL-Bank/GenBank/DDBJ public nucleic acid databases.

UniProtKB is a collaboration between the European Bioinformatics Institute, the Swiss Institute of Bioinformatics and the Protein Information Resource.

Using the database in Mascot 2.5 and later

Enable the predefined definition in Database Manager, which will download the required files automatically.

Using the database in Mascot 2.4

Enable the predefined definition in Database Manager to get the latest configuration. Downloading the files will fail, because Mascot 2.4 does not support HTTPS file downloads. Please download the FASTA file and required taxonomy files manually as described below.

Download (Mascot 2.3)

Expasy: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/
EBI: https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase

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

Version info: reldate.txt
TrEMBL Fasta file: uniprot_trembl.fasta.gz
TrEMBL Dat file: uniprot_trembl.dat.gz

To download TrEMBL updates automatically in Mascot 2.3 and earlier, the relevant definition block in db_update.pl is Trembl_complete_from_EBI.

Taxonomy (Mascot 2.3)

Taxonomy is identical to that for SwissProt, and is predefined in mascot.dat. Even if you have the Trembl Dat file, choose "SwissProt FASTA". In Mascot 2.3 and earlier, verify that the taxonomy definition in mascot.dat is up to date:

# TAXONOMY FOR SwissProt or Trembl from the fasta file Taxonomy_3 Identifier SwissProt FASTA Enabled 1 FromRefFile 0 DescriptionLineSep 0 SpeciesFiles NCBI:names.dmp, SWISSPROT:speclist.txt NodesFiles NCBI:nodes.dmp, NCBI:merged.dmp DefaultRule SWISSPROT, CHOP: ">[^_]*_\([^ ]*\) " 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.

The following taxonomy files are required:

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

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.

TrEMBL Release 2011_06 in Mascot 2.3 and earlier

A change in the format of speclist.txt broke taxonomy assignment in Mascot 2.3 and earlier for TrEMBL release 2011_06 onwards. The symptom is that searches using a taxonomy filter return no matches. A modified file that fixes the problem can be downloaded from this URL: speclist.txt.

If you use the database update script (db_update.pl) to perform automatic updates of TrEMBL, change the URL for downloading speclist.txt in the relevant definition block to http://www.matrixscience.com/downloads/speclist.txt. You also need to delete the old speclist.txt file just before running the update script, otherwise the downloaded file will be renamed to avoid a filename collision.

If you have discovered this problem after updating Trembl, the procedure to correct it is as follows:

Windows: stop the Mascot service, Unix: kill ms-monitor.exe
Delete the *.stats file in the database current directory
Download the modified speclist.txt to the taxonomy directory
Windows: start the Mascot service, Unix: execute ms-monitor.exe

Parse Rules (Mascot 2.3)

A typical Trembl Fasta title line is:

>tr|A0AQI4|A0AQI4_9ARCH Putative ammonia monooxygenase (Fragment) OS=uncultured archaeon GN=amoA PE=4 SV=1

You can use either the ID (A0AQI4_9ARCH) or the AC (A0AQI4) as the identifier.

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

The corresponding lines in the Dat file are:

ID   A0AQI4_9ARCH              Unreviewed;         206 AA.
AC   A0AQI4;

ID from Ref file: "^ID \([^ ]*\)"
AC from Ref file: "^AC \([-A-Z0-9_]*\)"

Configuration (Mascot 2.3 and earlier)

For this example, the database files were downloaded to C:\Inetpub\MASCOT\sequence\Trembl\current, decompressed using gzip, and renamed to Trembl_39.0.dat and Trembl_39.0.fasta.

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.

Mascot database maintenance utility

If you decide not to have the reference file locally, full text for individual entries can be retrieved across the web from Uniprot or an SRS server. For Uniprot, the required entries are:

Host: www.uniprot.org
Port: 80
Path: /uniprot/#ACCESSION#.txt
Parse rule: RULE_23 "\(.*\)"

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

This screen shot illustrates a configuration in which the identifier is AC, there is no local Dat file, and full text is retrieved from Uniprot: