Links

Search Engines & Data Bases

Protein and Gene Family Databases
CAZY		A large database describing the families of structurally related catalytic and carbohydrate-related binding modules and functional domains of enzymes that degrade, create or modify glycosidic linkages
EPD		The Eukaryotic Promoter Database is a resource that deals with Eukaryotic transcription regulation
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
MEROPS		A protease database
TC-DB		A transport protein database
TRANSFAC		A database on eukaryotic transcriptional regulation
Clustering Databases
ClusSTr		This database offers an automatic classification of Swiss-Prot and TrEMBL proteins into groups of related proteins
COG		The database of Clusters of Orthologous Groups of Proteins (COGs)
ProDom		ProDom provides automated analysis of protein domains
SYSTERS		Systers classifies the whole of Swiss-Prot and PIR into disjoint protein family clusters, which are then related as family and superfamily clusters.
ProtoMap		ProtoMap is an automatic classification of all Swiss-Prot and TrEMBL proteins that works with complete protein sequences
Protein Signature Databases
PROSITE		Prosite is a database of patterns and profiles
Pfam		Pfam is a collection of multiple protein sequence alignments and provides a good resource of models for identifying protein families, domains and repeats
SMART		The Smart database facilitate the identification and annotation of genetically mobile domains and the analysis of domain structures
TIGRFAMs		Tigrfams groups homologous proteins that are conserved with respect to function
BLOCKS		Blocks is a collection of multiply aligned ungapped segments corresponding to the most highly-conserved of proteins.
Integrated Derived Databases
iProClass		iProClass links ProClass, PIR-ALN, PROSITE, Pfam and Blocks into a single database providing family relationships and structural features of protein sequences
CDD		CDD is a database of domains derived from SMART, Pfam and contributions from NCBI LOAD (Library Of Ancient Domains) and use an algorithm to identify conserved domains in protein sequences
Interpro		Interpro integrates diagnostic protein signatures from PROSITE, PRINTS, Pfam, SMART and TIGRFAMs.
Arabidopsis Databases
ATTEND		Arabidopsis thaliana Tissue-specific Expression Database
TAIR		The Arabidopsis Information Resource
TDNA-Express		Arabidopsis gene mapping tool
Other Databases
CSB.DB		A Comprehensive Systems Biology Data Base
EUROCarbDB		The EUROCarbDB is a database and bioinformatics tool in the realm of glycobiology and glycomics that serves as a depository for carbohydrate related data similar to the extensively used data collections in the area of genomics and proteomics
MetaCyc		MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways from more than 300 different organisms
NCBI		National Center for Biotechnology Information (NCBI) creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information
PLACE		A database of plant cis-acting regulatory DNA elements
Literature Search
BIOSIS		BIOSIS delivers flexible information services - including databases and customized information products - to the global life sciences community
ISI Web of Knowledge		ISI Web of Knowledge is a dynamic, fully integrated environment that provides one source for high quality content and tools to access, analyze, and manage research information
PubMed		PubMed, a service of the National Library of Medicine, includes over 15 million citations for biomedical articles back to the 1950's