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Database Portals, Resources and Select Sequence Databases

 

 

Resources:

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bullet EBI, European Bioinformatics Institute, EBI Download site "The EBI is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures."
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bullet Expasy "The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE" Databases, Tools and Software Packages.
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bullet NCBI,  The National Center for Biotechnology Information "provides an integrated
approach to the use of gene and protein sequence information"  Databases and Tools
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bullet PIR Protein Information Resource "An integrated public resource of protein informatics to support genomic and proteomic research and scientific discovery." Located at Georgetown University.
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bullet Plant Genome Database (PlantGDB) Resource for Plant Comparative Genomics  
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bullet SIB, Swiss Institute of Bioinformatics "The SIB is an academic not-for-profit foundation established on March 30, 1998 whose mission is to promote research, the development of databanks and computer technologies, teaching and service activities in the field of bioinformatics, in Switzerland with international collaborations"
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bullet RESID Database (no longer) at the EBI  "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications." (quote form the RESID site)
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bullet UNIMOD  "Protein Modifications For Mass Spectrometry", A list of potential amino acid modifications and mass shifts.
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bullet UniProt The Universal Protein Resource " is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR."
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bullet What is FASTA format?  Protein ID programs use sequence databases (flat files) that are formatted  in FASTA format.  
 

Databases: ftp repositories

bullet IPI FASTA sequence databases (human, rat, mouse)  Stopped updating 2010.  The most notable characteristics of this repository is that IPI database  "maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases." 
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bullet NCBInr - The most widely used protein database in proteomics. Choose nr.gz  Other protein and nucleotide sequence databases at this site are: drosophila, ecoli, human, mouse, mitochondria, sts, est, swissprot
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bullet PIR-NREF, "a comprehensive database for sequence searching and protein identification, contains non-redundant protein sequences from PIR-PSD, Swiss-Prot, TrEMBL, RefSeq, GenPept, and PDB. Release 1.57, 22-Nov-2016, contains 1,891,871 entries."
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bullet Swiss-Prot - Located at Expasy.  One of the leading protein databases with minimal redundancy and the best annotation.  Uniprot_sprot.fasta.gz is the FASTA file, and uniprot_sprot.dat.gz  is the annotation file.
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bullet UNIMOD  Protein Modifications For Mass Spectrometry, another source for protein modification masses is Delta Mass at ABRF.

 

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