WOHL VIRION

CENTRE

ONLINE BIOINFORMATICS

 
 

Compiled by M.Mar Alba
Virus Genomics and Bioinformatics

NCBI: The National Centre for Biotechnology Information
EBI: European Bioinformatics Institute
UK MRC HGMP-RC: Human Genome Mapping Project
The Sanger Centre: Genome Campus, Hinxton
RSBS Bioinformatics: Research School of Biological Sciences, Canberra
NIH: National Institute of Health, US
ExPASy: Swiss Institute of Bioinformatics
BMERC: Biomolecular Engineering Research Center
EMBnet/CNB: Centro Nacional de Biotecnologia, Spain
SRCG: The Siberian Regional Center for Geneinformatics
Weizmann Institute of Science, Israel
PBIL: Pole Bio-Informatique Lyonnais
Bloomsbury Centre for Structural Biology, London

Sequence retrieval: Entrez (NCBI) Query GenBank database (NCBI) Sequence retrieval system (SRS, EBI) PDB search Swissprot (ExPaSy) Virus Database (UCL)

Homology-based search: BLAST(NCBI) Fasta (EBI) The PredictProtein server TGI (search ESTs)  PDB-ISL Server (search PDB)

Perform alignment: Clustalw at EBI Clustalw at Pasteur MultAlin Match-Box Lalign (2 sequences) Dialign2 (2 sequences) Blast2 (2 sequences) Jalview

Edit/Visualise alignment: Jalview CINEMA BoxShade

Define conserved blocks: Block Maker Meme Sequence Logo Generation

InterPro (EBI)
Prosite (ExPaSy)
Blocks (Fred Hutchinson Cancer Research Center)
Pfam (The Sanger Centre)
Prodom (INRA, Toulouse)
SMART (EMBL)
PRINTS (University of Manchester)
DOMO (J.Gracy/P.Argos)
Hidden Markov Models: theory
HMMER 2.1.1: to build up HMMs
Hidden Markov Models: links

Compute pI: Compute pI/Mw  (Luca Toldo)	Design primers: Oligo Design Oligo calculator (MW,composition,Tm..) Primer design (Luca Toldo) Primer3	Translate DNA sequence: Translate into all possible ORFs (Luca Toldo) TranslatER: Translate a DNA sequence Java Ribosome: translate DNA sequence into protein ORF finder at NCBI
Manipulate sequences: Reverse and complement sequences (Luca Toldo) Randomize a sequence (Luca Toldo) Reverse Complement of Sequence	Protein properties: SAPS: Statistical Analysis of Protein Sequences  ProtScale: hydrophilicity/hydrophobicity	Convert sequence file format: READSEQ: Sequence Format Conversion
DotPlot: Dotter: a dot-matrix program to analyse repetitive sequences DOTPLOT (Luca Toldo)	Find restriction sites: Webcutter Pattern searching	Convert multiple alignment format: ClustalW - format conversion facility

Databases: PDB (Protein Data Bank) CATH (UCL) SCOP (MRC-LMB) FSSP (EBI)

Structure prediction: JPred (EBI) PREDATOR (EMBL) AGADIR (EMBL) HNN (Pole Bio-Informatique Lyonnais) PSIpred (Warwick) SwissModel (ExPaSy) CPH (Technical University of Denmark)

TIGR: The Institute for Genomic Research
Proteome Inc. (YPD, WormPD)
MIPS: Munich Information Center for Protein Sequences
Stanford genomic resources (SGD,ATdb)
KEGG Genomes: Kyoto Encyclopedia of Genes and Genomes
MAGPIE: Automated Genome Project Insvestigation Environment
GOLD v.1.0: Genomes On Line Database
Genethon: Human Genome Research Centre
GDB: Human Genome Database
Herpesvirus genomes (UCL)
Genome analysis (MRC LMB)

WebGene: CNR, Milan
Grail: Oak Ridge National Laboratory
Gene Finder: The Sanger Centre
GeneID: Genome Informatics, IMIM

 

Protein interactions and metabolic pathways

DIP: Database of Protein Interactions
INTERACT (Manchester,UK)
KEGG: Kyoto encyclopedia of genes and genomes
EcoCyc: E.coli genes and metabolism
MIPS: yeast pathways
Transpath: signal transduction database
CSNDB: Cell signaling
 

Prediction of binding sites: MatInspector: binding site prediction  TESS: binding site prediction Promoter Scan: promoter prediction Signal Scan TFBIND PROMO The Promoter Database of  Saccharomyces cerevisiae	Find conserved sites: MEME: pattern discovery Pratt: Find patterns  YEBIS: pattern discovery Yeast tools: find patterns, etc. Jaak Vilo homepage: expression, clustering, patterns	Related databases: TRANSFAC: Transcription Factor Database EPD: Eukaryotic Promoter Database  Genome-Wide Expression: Young's lab TRRD: Transcription Regulatory Regions Database, Nobosibirsk GeneExpress system, Nobosibirsk TRADAT: TRAnscription Database and Analysis Tools Plant CARE: plant cys-acting regulatory elements Muscle-Specific Regulation of Transcription
Gene expression clustering CLUSTER (University of Stanford) Clustering Methods Bibliography

SIMPLE v.3.0: simple sequences
satellites: identifies satellites and periodic repetitions
repeats: microsatellite-type regions

WebPHYLIP
Web Resources in Molecular Evolution and Systematics

CPAN Perl
Bioperl

Royal Society
Wellcome Trust
ICREA (Catalonia)
Ministerio de Ciencia y Tecnologia (Spain)

 
Biology WorkBench 3.1
FASTA format description
ACUTS
Computational Biology or Bioinformatics references
The Statistics of Sequence Similarity Scores
Bioinformatics WWW Sites
AltaVista: search engine
Amazon: books, etc.
UK street map
The Origin of Species, Charles Darwin
The Bioinformatics Resource
Rupert Sheldrake Online
alggen
Statistics programs
Gene Ontology (fly,mouse,yeast)
Sunsite (GNU, downloads)

M. Mar Alba, last updated June 22 2001