Swissprot Database

From bwHPC Wiki
Jump to: navigation, search

The main documentation is available via module help dbdata/swissprot on the cluster. Most software modules for applications provide working example batch scripts.


Description Content
module load dbdata/swissprot
License Public Domain | Free for academic users
Citation Publications on Uniprot/Swissprot
Links Nucleic Acids Research | N.A.R.-Oxford Journals
Graphical Interface No
Update Daily at midnight

1 Description

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include format and content enhancements, cross-references to additional databases, new documentation files and improvements to TrEMBL, a computer-annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDSs) in the EMBL Nucleotide Sequence Database, except the CDSs already included in SWISS-PROT. We also describe the Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT.

More detailed information about the SWISS-PROT Database

2 License

Public Domain

3 Updates

On the bwUniCluster, SWISS-PROT is updated daily at midnight.

3.1 Update-Date

You can check the date of the latest update by using
'module whatis dbdata/swissprot/current' or 'module help dbdata/swissprot/current'.

  • $ module whatis dbdata/swissprot/current

dbdata/swissprot/current: This packages contains the Nucleic Acids Protein Sequence
  Database Swiss-Prot. Last update: 24.11.2015

  • $ module help dbdata/swissprot/current

Module Specific Help for 'dbdata/swissprot/current'
DESCRIPTION
SWISS-PROT is a curated protein sequence database which strives
[...]
Last update: 24.11.2015
[...]

3.2 Exeptions

Updates will be avoided if:

  • the current database version is in use by a module. E.g. module load dbdata/swissprot/current was called by another module and has still not finished its job,
  • there is no newer version available at the source system.

3.3 Update-Source and Logs

Source: ftp.ncbi.nih.gov/blast/db/swissprot.tar.gz
Logs: in $SWISSPROT_HOME you'll find some logfiles.

$ ls -x $SWISSPROT_HOME 
bwhpc-examples cron.out          lastupdate.txt   ...

lastupdate.txt : Informations about the last successful or not successful updates including date and time.

4 Usage

4.1 Program Binaries

There will be no binary packages supplied with the database.
It's a link to DB-files using environment-variables you can include in your submit-scripts for other modules.
After loading the SWISS-PROT module (module load dbdata/swissprot/current) this path is also set to the local $PATH- and other environments.

4.2 Extensions

Extension Content Format
Protein database formatted without "-o T"
phr deflines binary
pin indices binary
psq sequence data binary
Protein database formatted with "-o T" add these ISAM files:
pnd GI data binary
pni GI indices binary
psd non-GI data binary
psi non-GI indices binary

Please report missing entries and errors to Rainer Rutka.