The Steve Jackson Laboratory Website
Transformative discoveries in genome and cellular integrity

Scientific

Molecular biology databases & search tools.


Portals and Genome Browsers


Model Organism Databases


DNA Sequence Analysis


Multiple Alignment Tools

  • Clustal Omega Clustal Omega is a new multiple alignment sequence program that uses seeded guide trees and HMM profile-profile techniques to generate alignments.
  • PROMALS, constructs multiple protein sequence alignments using information from database searches and secondary structure prediction.
  • T-Coffee

Other sites of interest

Proteomics and Protein Sequence Analysis

  • CBC Prediction Servers Protein Function Analysis
  • CompPASS Database - Harper Lab Proteomic Database. This site contains all of the IP-MS/MS data from the following papers:
    • The Human DUB Interactome (Sowa et al., Cell, 2009)
    • The Human Autophagy Pathway (Behrends et al., Nature, 2010)
    • The Human ERAD Pathway (Christianson et al., Nature Cell Biology, 2011)
  • ELM The Eukaryotic Linear Motif resource for Functional Sites in Proteins
  • ExPASy Proteomic tools
  • Fugue, a fold recognition method using structural environment-specific substitution tables and structure-dependent gap penalties
  • Integrated Protein Domains InterProScan
  • NetPhosYeast, predicts serine and threonine phosphorylation sites in yeast proteins.
  • PaxDb. Protein abundance database.
  • Phosida, phosphorylation site database. Phosida allows retrieval of phosphorylation data of any protein of interest. It lists phosphorylation sites associated with particular projects and proteomes or, alternatively, displays phosphorylation sites found for any protein or protein group of interest.
  • Phospho.ELM. A database of S/T/Y phosphorylation sites
  • Phosphosite, an expert curated knowledgebase of protein phosphorylation
  • Phyre, Protein Homology/analogY Recognition Engine
  • PRIDE Archive. The PRIDE PRoteomics IDEntifications (PRIDE) database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence.
  • ProteomicsDB, proteomics database setup to enable users to explore and analyse human proteome data.
  • Proteopedia - wiki-based interactive 3D encyclopaedia of proteins and molecules
  • PSIPRED - protein structure prediction server
  • Saccharomyces cerevisiae Phosphorylome database.
  • SCDFinder - a web-based tool for the identification of putative novel ATM and ATR targets
  • Simple Modular Architecture Research Tool (SMART), protein domain finder
  • STRING - STRING is a database of known and predicted protein interactions.

Protein mutation prediction software

  • Mutation Taster: A free web-based application to evaluate DNA sequence variants for their disease-causing potential
  • PPopen: Predicts all possible amino acid subsitutions for a protein of interest
  • Provean: PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.
  • SIFT: predicts whether an amino acid substitution affects protein function.
  • Polyphen2: A tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.
  • Yeastmine: an integrated data warehouse for Saccharomyces cerevisiae data as a multi-purpose toolkit.

Whole Genome Analyses

  • Biogrid. A curated set of physical and genetic interactions.
  • iHOP, information hyperlinked over proteins
  • NDEx public server, the Network Data Exchange
  • TheCellMap.org, a central repository for quantitative genetic interaction data for Saccharomyces cerevisiae
  • Yeast interactome. A Physical Interactome Map of Saccharomyces Cerevisiae.


DNA repair sites