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Links

A few selected links relevant to this project and pathogenomics...

Microarray Analysis

• Comprehensive Microarray Resource

Genome Databases

• GOLD: Genomes Online Database

• Genome Databases (NCBI)

• Prominent Organisms Taxonomy list (NCBI)

• Model Organisms Resources Links (Sanger Institute)

• A Guide to Sequenced Genomes (Genome News Network)

• Publication List of Complete Genomes

• Acedb

• UCSC Genome Bioinformatics

• Ensembl

• Human Genome Projec
  

• TIGR Microbial Genomes

• Microbial Genome Database

• Comprehensive Microbial Resource

• Parasite Genome Databases (EBI)

• Parasite Webtools

• Viral Genome Database (Chris Upton)

• Viral Genomes (NCBI)

• HIV Database

• viruloGenome

Signal Transduction and Metabolic Networks

• MetaCyc (Metabolic Pathway Database)

• Pathway Tools Software – metabolic pathway analysis of genomes

• BioCyc – a collection of Pathway/Genome Databases.

• KEGG Pathway Database

• 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

• BacBix Database of Virulence Factors (click on database)

• 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

• Neural Network Prediction of OMPs

• Unibo-Predictors 

• 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.

• Prediction of secreted proteins

Homology or motif-based analyses tools

• NCBI BLAST2

• WU-BLAST2

• Fasta search

• PSI-BLAST

• PHI-BLAST (Pattern-Hit Initiated BLAST)

• BLAT

• SSEARCH

• MOTIFS

• FINDPATTERNS

• VAST

• InterPro

• PROSITE

• Pfam HMM

• BLOCK Search Tools

• PRINTS

• ProDom

• SMART

• TIGRFAM

  
  

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Nucleic Acid Pattern Search

• Fuzznuc (EMBOSS)

• FINDPATTERNS

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

• SNP Consortium Database

• dbSNP

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

• ENTREZ

• SRS

Multiple Alignment Tools

• CLUSTALW

• CLUSTALX

• TCOFFEE

Profile and HMM search Tools

• HMMer

• BLOCK Search Tools

• Pfam HMM

Translate DNA and other basic tools

• EXPASY

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

• REBASE

• Webcutter

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