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Links
A few selected links relevant to this project and pathogenomics...
Microarray Analysis
Genome Databases
Signal Transduction and Metabolic Networks
Pathway Tools Software metabolic pathway analysis of genomes
BioCyc a collection of Pathway/Genome Databases.
BioCarta Web based resource of information on gene function and proteomic pathways.
Cell Signaling Networks Database a data- and knowledge- base for signaling pathways of human cells.
Transpath database on signal transduction networks.
MINT database designed to store functional interactions between biological molecules
BIND Biomolecular Interaction Network Database
Identification of pathogenicity islands, virulence factors, and related comparative
genome analysis
Island Path Aids identification of pathogenicity islands and other genomic islands
Artemis Comparison Tool (ACT) - Comparative sequence viewer and annotation tool
EnteriX Visualization of enterobacterial genomes (see also the links to Maj amd Menteric within...)
SEEBUGS Substractive and concordant comparison of genomes
Prediction of Subcellular Localisation (SCL) of Proteins
Prediction of Possible Surface-Exposed Membrane Proteins:
PSORT-B Prediction of SCL of proteins in Gram negative bacteria
PSORT Prediction of SCL of proteins in prokaryotes
HMMTOP Prediction of transmembrane helices and topology of proteins
TMHMM Prediction of transmembrane helices
DAS Transmembrane Prediction
TMpred Prediction of Transmembrane Regions and Orientation
SOSUI Classification and Secondary Structure Prediction of Membrane Proteins
TMAP - Prediction of Transmembrane Segments in Proteins
TopPred 2 Topology Prediction of Membrane Proteins
Beta-Barrel Finder -Download BBF program
Prediction of Secreted Proteins:
PSORT Prediction of SCL of proteins in prokaryotes
PSORT-B Prediction of SCL of proteins in Gram negative bacteria
PSORT II - Prediction of SCL of proteins in eukaryotic organisms
iPSORT SCLsite predictor for N-terminal sorting signals in eukaryotes
TargetP - Prediction of SCL of proteins in eukaryotic organisms
SignalP Prediction of signal peptide cleavage sites
SubLoc Prediction of protein SCL by support vector machine
NNPSL for both eukaryotic and prokaryotic organisms
Domain Projection Method Classification of protein domains and sequences by subcellular localisation into nuclear, cytoplasmic and secreted locales.
Homology or motif-based analyses tools
PHI-BLAST (Pattern-Hit Initiated BLAST)
Nucleic Acid Pattern Search
Fuzznuc (EMBOSS)
Identification of Antigenic Sequences
SYFPEITHI database of peptide sequences, anchor positions, MHC specificity
JenPep database of quantitative binding data for immunological protein-peptide interactions
IMGT - the international ImMunoGeneTics information system
ANTIGENIC: EMBOSS finds antigenic sites in proteins
nHLAPred for prediction of MHC binding peptides
ProPredI for identifying the MHC Class I binding regions in antigens
BCIPEP B cell epitopes
MHCBN database of MHC binding and non-binding peptides
MHCPEP peptide sequences known to bind MHC molecules
FIMM database of functional immunology, focusing on MHC, antigens, and diseases
MAPPP MHC-I Antigenic Peptide Processing Prediction
RANKPEP prediction of binding peptides to Class I and Class II MHC molecules
PREDEP MHC Class I epitope prediction
CTLPred a SVM & ANN based CTL epitope prediction tool
ProPred MHC Class II binding peptide prediction
EPIPREDICT - predict HLA Class II restricted T cell epitopes and antigens
Human Polymorphisms Associated with Infectious Diseases
SNPDB single nucleotide polymorphism database
Phred/Phrap/Consed System - visualization and analysis of sequences and SNPs
Promoters
and Regulatory Motif analysis
DBTBS - Database of Bacillus subtilis promoters and transcription factors
EPD Eukaryotic promoter database
Prodoric Prokaryotic database of gene regulation and regulatory networks.
PromEC Database of E.coli promoters
TRANSFAC Eukaryotic transcription factor database
Consite Prediction of transcription factor binding sites in eukaryotic sequences using phylogenetic footprinting
AraC-XylS Database of bacterial helix-turn-helix transcription factors
RegulonDB Database on E.coli transcriptional regulation and genome organization
DPInteract Database on E. coli DNA-protein interactions.
Finding Sequences in Public Databases
Multiple Alignment Tools
Profile and HMM search Tools
Translate DNA and other basic tools
Structure Databases
SCOP Structural Classification of Proteins
CATH Protein Structure Classification at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily(H)
Restriction Enzymes
Other Relevant Innate Immunity Research Group
Septic Shock - The National Institute of Allergy and Infectious Diseases funded systems approach to innate immunity-inflammation-sepsis
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© 2002 Functional Pathogenomics of Mucosal Immunity . . . A Genome Prairie Project