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Table 1 List of databases/programs in PIPA

From: The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation

Method/Database

Description

Website*

CatFam

Enzyme profile databases based on three- and four-digit EC numbers

developed by our group

CDD

NCBI Conserved Domains Database

[9]

COG

Clusters of Orthologous Groups of proteins

[39]

Pfam +

Hidden Markov Models of protein domains and families

[40]

TIGRfam +

Hidden Markov Models of curated protein families

[41]

SMART +

Identification and annotation of genetically mobile domains

[42]

Gene3D +

Protein families with structural information

[43]

FprintScan +

Program that searches the protein fingerprint database PRINTS

[44]

PANTHER +

Proteins classified by experts into families and subfamilies

[45]

SUPERFAMILY +

Structural assignments to protein sequences at the superfamily level

[46]

ProDom +

Automatically generated protein domain families

[47]

PIR +

Integrated Protein Informatics Resource

[48]

PROSITE +

Database of protein domains, families and functional sites

[49]

COILS +

Prediction of coiled-coil regions in proteins

[50]

Phobius

A combined transmembrane topology and signal peptide predictor

[51]

PSORTb

Prediction of the subcellular localization of bacterial proteins

[52]

  1. *Accessed on July 13, 2007
  2. +Integrated from InterPro
  3. PIPA currently integrates 16 programs/databases that are either developed by our group (CatFam) or publicly available.