Literature Searching | Protein Analysis | Motif Discovery and Analysis
Molecular Interaction and Pathway Databases | Gene Expression Analysis
Some links to useful tools from other groups are provided on this page.
NCBI PubMed
A service of the U.S. National Library of Medicine and a resource for molecular biology information. PubMed includes scientific journal articles from MEDLINE and many other life science journals.
SLoop Database (No longer avaliable)
Predicting/identifying loops in proteins.
Click HERE to see the current list of databases provided by the Biochemistry Department at the University of Cambridge.
MolMovDB
A database of macromolecular movements with associated tools for flexibility and geometric analysis.
Pfam
Protein family database.
Blocks
Protein database of conserved motifs, or blocks.
PRINTS
Protein database of conserved motifs, or prints.
PROSITE
Protein family and domain database.
CATH Protein Structure Classification
Protein structure classification database.
SCOP: Structural Classification of Proteins
Structure classification database.
SFLD: Structure-Function Linkage Database
Links evolutionarily related sequences and structures from mechanistically diverse superfamilies of enzymes to their chemical reactions.
BLAST
Blast multiple sequence alignment tool.
IPI - International Protein Index
An EMBL-EBI database that provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms.
PICR - Protein Identifier Cross-Reference Service
A protein ID cross-reference database tool by EMBL-EBI.
MEME: Multiple Em for Motif Elicitation
A tool for the discovery of DNA or protein motifs/patterns.
BioGRID
A general repository for molecular interactions from multiple species.
KEGG
A collection of manually drawn pathway maps representing the current knowledge on molecular interactions and reaction networks.
BioCarta
A pathway database with accompanying analysis tools.
STRING
A database of known protein-protein interactions with an application that integrates interaction data from multiple sources such as literature, experiemntation and genomic context with an intuitive visualization of retrieved networks.
STICH
A project related to STRING. A database that integrates known protein-chemical interactions from various sources with an intuitive visualization of retrieved networks.
BIND
The Biomolecular Interaction Network Database is part of BOND and contains molecular interactions from high-throughput technologies and hand curration of the literature.
IntAct
IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.
CAGED: Cluster Analysis of Gene Expression Dynamics (No longer publically avaliable)
Cluster analysis software for gene expression data.
Click HERE for more information.
BicAT: Biclustering Analysis Toolbox
Cluster analysis software for gene expression data.
HCE: Hierarchical Clustering Explorer
Interactive exploration of hierarchically clustered data including gene expression data.
MeV: MultiExperiment Viewer
Tools for the analysis of microarray data including statistical analysis, clustering and more.
SAM: Significance Analysis of Microarrays
MS Excel plugin for the statistical analysis and filtering of microarray data.
GEPAS: Gene Expression Pattern Analysis
Suite of tools for the analysis of microarray data including normalization, preprocessing, filtering, clustering and more.
BioConductor
An open source software project that provides statistical and graphical methods for the analysis of genomic data.
DAVID: Database for Annotation, Visualization and Integrated Discovery
A set of tools for the functional analysis of gene annotations.
G-SESAME: Gene Semantic Similarity Analysis and Measurement Tools
Tools for the semantic analysis of gene annotations.
