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Protein Bioinformatics

Protein regulation, protein localization, protein motifs, protein expression, protein structure, post-translational modifications of protein, protein interactions, and protein function are important because proteins constitute the largest functioning entity inside the cell. Proteomic Bioinformatics is thecollection, organization and analysis of large amounts of proteomic data, using networks of computers and databases.

Getting Started with Protein Bioinformatics

You must start with your protein sequence. To obtain the sequence of your protein do the following. Visit the following links and search for the protein you are studying.

Protein sequence databases are categorised as primary, composite or secondary. Primary databases contain protein sequences and function as a repository for raw data.

Search for Proteins and Protein Sequences using:

Protein Primary Amino Acid Sequence
Physical or Chemical Properties
Nucleotide Sequences
Peptide Sequences
Text Strings

Search for Proteins using Protein Primary Amino Acid Sequence

PepSea - Protein identification by searching a sequence

Search for Proteins using Physical or Chemical Properties

MassSearch: - Search SwissProt or EMBL Databases by protein mass after digestion at ETH-Zürich
TagIdent: - Retrieve SwissProt proteins given pI and Mw at ExPASy
AACompIdent -is a tool which allows the identification of a protein from its amino acid composition. It searches the Swiss-Prot and / or TrEMBL databases for proteins, whose amino acid compositions are closest to the amino acid composition given.

Search for Proteins by Using Nucleotide Sequences

BLAST (BLAST: Basic Local Alignment Research Tool) (NCBI)
BEAUTY (BLAST Enhanced Alignment Utility)

Search for Proteins Using Peptide Sequences

BLAST (BLAST: Basic Local Alignment Research Tool) (NCBI)
Aldente Identify proteins with peptide mass fingerprinting data. A new, fast and powerful tool that takes advantage of Hough transformation for spectra recalibration and outlier exclusion
PepSea - Protein identification by peptide mapping or peptide sequencing from Protana, Denmark.
MultiIdent tool - Identify proteins with pI , Mw , amino acid composition, sequence tag and peptide mass fingerprinting data

Search for Proteins by Using Text Strings

Integr8

Entrez-Pubmed Protein Query

Protein sequence - primary sequence of proteins (primary)

SWISS-PROT
PIR-International
Entrez-Pubmed Protein Query

Protein sequence (secondary)

Secondary databases contain information derived from protein sequences and help the user determine whether a new sequence belongs to a known protein family.

PROSITE
PRINTS
Pfam

Protein sequence (composite)

Composite databases such as OWL and the NRDB compile and filter sequence data from different primary databases to produce combined non-redundant sets that are more complete than the individual databases and also include protein sequence data from the translated coding regions in DNA sequence databases.

OWL
NRDB


 

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