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MIPS resources

http://mips.gsf.de/

Description :
Databases at Munich Information Center for Protein Sequences

PIR - Protein Information Resource

http://pir.georgetown.edu/

Description :
The Protein Information Resource (PIR) is an integrated public bioinformatics resource that supports genomic and proteomic research and scientific studies. PIR has provided many protein databases and analysis tools to the scientific community, including the PIR-International Protein Sequence Database (PSD) of functionally annotated protein sequences. Because the protein sequence database activities of PIR, Swiss-Prot, and TrEMBL are now combined to produce UniProt databases, the PIR-PSD is no longer being updated. Release 80.00 (31-Dec-2004), the final release for PIR-PSD, is available for ftp download and online searching at the PIR website. All PIR-PSD entries have been merged into the UniProt databases and PIR-PSD identifiers can be used to retrieve and track these sequences in either UniProtKB or UniParc. PIR contributes to the functional annotation of UniProtKB protein sequences. Major ongoing annotation efforts include curation of protein families in the PIRSF (SuperFamily) system, definition of classification-driven rules for the propagation of position-specific features, protein names, and GO terms to protein entries, as well as bibliographic attribution of experimental features. A new PIR resource iProLINK provides multiple annotated literature corpora to facilitate text mining research in the area of literature-based database curation, named entity recognition, and protein ontology development. PIR continues to enhance iProClass, an integrated database of protein family, function, and structure information and a hub for mapping and integrating protein data from multiple sources, and maintains PIR-NREF, a non-redundant reference database of protein sequences.

The PIR web site connects data mining and sequence analysis tools to underlying databases for information retrieval and knowledge discovery, with functionalities for interactive queries, combinations of sequence and annotation text searches, and sorting and visual exploration of search results. The FTP site provides free download for database releases.

Recent develoments :
Recent developments for the UniProt, PIRSF, iProClass, and PIR-NREF databases are described individually in this on-line Database Collection.

Aknowledgement :
The PIR is supported by NIH grant U01-HG02712 and NSF grants DBI-0138188 and ITR-0205470.

References :
Wu, C.H., Yeh, L.S., Huang, H., Arminski, L., Castro-Alvear, J., Chen, Y., Hu, Z., Kourtesis, P., Ledley, R.S., Suzek, B.E., Vinayaka, C.R., Zhang, J. and Barker, W.C. The Protein Information Resource. Nucleic Acids Res. 2003 Jan 1;31(1):345-7.

UniSave

http://www.ebi.ac.uk/uniprot/unisave/

Description :
The UniProtKB Sequence/Annotation Version database (UniSave) is a comprehensive archive of UniProtKB/Swiss-Prot a nd UniProtKB/TrEMBL entry versions. All changed Swiss-Prot and TrEMBL entries are loaded into the UniSave as part of the public UniProtKB releases. Unlike the UniProtKB, which contains only the latest Swiss-Prot and TrEMBL entry versions, the UniSave provides access to previous versions of these entries.

Aknowledgement :
UniProt is mainly supported by the National Institutes of Health (NIH) grant 1 U01 HG02712-01. Minor support for the EBI s involvement in UniProt comes from the two European Union contracts BioBabel (QLRT-2000-00981) and TEMBLOR (QLRI-2001-00015) and from the NIH grant 1R01HGO2273-01. Swiss-Prot activities at the SIB are supported by the Swiss Federal Government through the Federal Office of Education and Science. PIR activities are also supported by the National Science Foundation (NSF) grants DBI-0138188 and ITR-0205470.

References :
1. Leinonen R., Nardone F., Zhu W. and Apweiler R. (2006). UniSave: the UniProtKB Sequence/Annotation Version database. Bioinformatics, 22(10):1284-1285.

PPT-DB

http://redpoll.pharmacy.ualberta.ca/PPT_DB/public_html/PPT_main.html

Description :
Protein Property Prediction and Testing Database

MitoRes

http://www2.ba.itb.cnr.it/MitoRes/

Description :
MitoRes [1] is an update of the MitoNuc database [2], extensively modified in its structure, data sources and graphical interface. MitoRes has been developed with the aim to provide a comprehensive, integrated and non-redundant resource for functional and comparative studies supporting research on basic science of mitochondria. The database contains data on nuclear-encoded mitochondrial proteins in Metazoa and provides comprehensive sequence datasets (gene, transcript and protein) as well as useful tools for their extraction and export. In addition, MitoRes clusters proteins on the basis of their sequence similarity and interconnects them with genomic data. A search engine and sequence management tools allow the query/retrieval of the database content and the extraction and export of sequences and related sub-sequences (intron, exon, UTR, CDS, signal peptide and gene flanking regions) ready to be used for in silico analysis.

Recent develoments :
Changes recently introduced with respect to the last published version of the MitoNuc database have concerned (1) database structure, (2) data sources, (3) database content, (4) updating procedures (5) Web interface and (6) query/retrieval tool. More details are provided in the on-line Manual accessible by the database Home page.

Aknowledgement :
This work has been supported by 'Ministero dell’Istruzione, dell’Università e della Ricerca’ (MIUR), Italy, within the grants of PNR 2001-2003 (FIRB art.8) D.M. 199, Strategic Program: Post-genome, grant 31-063933; FIRB 2003 art. 8 D.D. 2187 del 12-12-2003 LIBI.

References :
1. Catalano D, Licciulli F, Turi A, Grillo G, Saccone C, D'Elia D. MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa. BMC Bioinformatics, 2006 7:36
2. Attimonelli M, Catalano D, Gissi C, Grillo G, Licciulli F, Liuni S, Santamaria M, Pesole G, Saccone C. MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002. Nucleic Acids Res. 2002, 30: 172-173

OrthoDB

http://cegg.unige.ch/orthodb/browse

Description :
An hierarchical catalog of orthologous proteins in metazoa

PairsDB

http://pairsdb.csc.fi/

Description :
Pairwise alignments of all sequences in UniProt

Protein Clusters

http://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters

Description :
Related protein sequences (clusters)of Reference Sequence proteins encoded by complete genomes

UCSD-Nature Signaling Gateway Molecule Pages

http://www.signaling-gateway.org/molecule/

Description :
Expert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling

CPDB

http://sarst.life.nthu.edu.tw/cpdb/

Description :
The circular permutation database

AlterORF

http://www.cienciavida.cl/alterorf/

Description :
Database of alternate open reading frames

Bionemo

http://bionemo.bioinfo.cnio.es/

Description :
Curated information about biodegradation-related genes and proteins

The Cell Cycle DB

http://www.itb.cnr.it/cellcycle

Description :
Genes and proteins involved in human and yeast cell cycle

SuperTarget and Matador

http://insilico.charite.de/supertarget

Description :
Drug-related information: medical indications, adverse drug effects, drug metabolism and GO terms of the target proteins

ExPASy Molecular Biology Server

http://www.expasy.org/

Description :
Expert Protein Analysis System; programs and databases for the analysis of protein sequences, structures and 2-D PAGE.

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