UniProt: the Universal Protein knowledgebase
The Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt), which is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces.
InterProScan - an integration platform for the signature-recognition methods in InterPro
The Perl-based InterProScan implementation is available from the EBI ftp server (ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/) and the SRS-basedInterProScan is available upon request.
InterProScan: protein domains identifier
InterProScan is a tool that combines different protein signature recognition methods from the InterPro consortium member databases into one resource and can be analysed for protein as well as DNA sequences.
The Universal Protein Resource (UniProt)
During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; the UniProt keyword list got augmented by additional keywords; the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications.
The SWISS-PROT protein sequence data bank and its supplement TrEMBL
This supplement consists of entries in SWiss-PROT-like format derived from the translation of all coding sequences in the EMBL nucleotide sequence database, except the CDS already included in SWISS- PROT.
ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination
The PX submission tool simplifies the process of submitting data to PRIDE by automating the very labor-intensive and therefore time-heavy and expensive process of manually downloading and editing files.
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
The SWISS-PROT protein knowledgebase connects amino acid sequences with the current knowledge in the Life Sciences by providing an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions.
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
Pindel, a pattern growth approach, is presented, to detect breakpoints of large deletions and medium-sized insertions from paired-end short reads and to demonstrate the efficiency of the computer program and accuracy of the results.
InterPro: the integrative protein signature database
The InterPro database integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs.
Evaluation of methods for the prediction of membrane spanning regions
This work presents an evaluation of the performance of the currently best known and most widely used methods for the prediction of transmembrane regions in proteins and shows that TMHMM is currently the best performing trans Membrane prediction program.