HUSAR Bioinformatics Lab
Deutsches Krebsforschungszentrum Genomics Proteomics Core Facility
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ATTENTION: Change of default HUSAR server if you use the links on our website
Update of the ChipSeq Analysis Pipeline ChiPeAn (Version 2.0)
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Topics:
  1. Data Submission
  2. FTP Repositories
  3. Major Research and Genome Centres
  4. Access to Remote Databases and Applications
  5. Gene Prediction Tools
  6. Resources for Microarray Analysis
  7. Resources for Protein Analysis
 

 
 
Data Submission:
 

 
FTP Repositories:
 

 
Major Research and Genome Centres:
  • EBI, the European Bioinformatics Institute in Hinxton, UK.
  • EMBL, the European Molecular Biology Laboratory.
  • Sanger Centre. A major UK genome research centre.
  • NCBI, the National Center for Biotechnology Information (USA).
  • TIGR The Institute for Genomic Research (USA).
  • GVPN/Genethon: Centre de Recherche sur le Génome Humain.
  • ExPASy at the University of Geneva.
  • The Jackson Laboratory. Scope: mammalian genetics.
  • GenomeNet WWW server, Japan. Includes the KEGG metabolic database.
  • BiSC, the Bioinformatics Supercomputing Centre in Toronto.
  • KECK, The W.M. Keck Center for Computational & Structural Biology (Texas).
  • LANL, biological sciences at the Los Alamos National Laboratory.
  • JGI, the Dept. of Energy's Joint Genome Institute.
  • NCGR, the National Center for Genome Resources (USA).
  • NIH, the US National Institutes of Health.
  • Pasteur Institute. Major French research organization.
  • Cold Spring Harbor Laboratory , a major cell biology research centre.
  • SHGC, the Stanford Human Genome Center.
  • ANGIS, the Australian National Genomic Information Service.
  • Weizmann Institute, Israel. Bioinformatics and Biological Computing.
  • IMB, Institut für Molekulare Biotechnologie, Jena.
 

 
Access to Remote Databases and Applications:
 

 
Gene Prediction Tools:
  • BCM Search Launcher. Molecular biology-related search and analysis services available on the WWW by providing a single point-of-entry for related searches.
  • DoubleScan is a program for comparative ab initio prediction of protein coding genes in mouse and human DNA.
  • FGENE software collection from softberry (origin Sanger Inst.).
  • GENEBUILDER is an integrated computing system for protein-coding gene prediction.
  • GeneID is an Artificial Intelligence system for predicting vertebrate gene structure.
  • GeneMachine performs both comparative and predictive gene identification.
  • Genemark relies upon an Inhomogeneous Markov Model to predict genes.
  • Genesplicer detects splice sites in the genomic DNA of various eukaryotes.
  • GeneWise2 compares a protein sequence to a genomic DNA sequence.
  • GenomScan predicts the locations and exon-intron structures of genes in genomic sequences incorporating protein homology information.
  • GENSCAN is a program designed to predict complete gene structure including exons, introns, promoter and poly-adenylation signals, in genomic sequences. It differs from the majority of existing gene finding algorithms in that it allows for partial genes as well as complete genes and for the occurrence of multiple genes in a single sequence, on either or both DNA strands.
  • GENSCAN can also be accessed here.
  • Glimmer is a system for finding genes in microbial DNA and uses Markov models.
  • GlimmerM is a gene finder derived from Glimmer, but developed specifically for eukaryotes.
  • GrailEXP is a software package that predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements.
  • HMMGENE, prediction of vertebrate and C. elegans genes.
  • MetaGene 2.6 allows the researcher to submit sequences to seven gene prediction engines simultaneously to obtain a comprehensive report on sequence features.
  • MZEF is Michael Zhang's Exon Finder.
  • NETGENE2, intron splice site prediction in human, C. elegans and A. thaliana DNA.
  • NetPlantGene, intron splice sites in Arabidopsis thaliana DNA.
  • NETSTART. Translation start in vertebrate and A. thaliana DNA.
  • NNSPLICE: Splice Site Prediction by Neural Network.
  • ORF Finder is a graphical analysis tool to find open reading frames.
  • PredictGenes: predict and verify gene structure by alignment with homologous proteins.
  • PROMOTER. Transcription start sites in vertebrate DNA.
  • Promoter Inspector. Several tools from the Genomatix.
  • PromoterScan predicts promoter regions based on scoring homologies.
  • SplicePredictor, a method to identify potential splice sites in (plant) pre-mRNA.
  • TESS finds transcription elements.
  • The GeneSeqer: a method to identify potential exon/intron structure in pre-mRNA by splice site prediction and spliced alignment.
  • The ORF Finder is a graphical analysis tool.
  • tRNAscan searches for tRNA genes in genomic sequences.
  • TWINSCAN exploits the patterns of conservation observed in alignments between a target genomic sequence and its homologous sequence in other organisms.
  • Yeastgene calculates the YZ value of an ORF or a fragment of DNA sequence in Saccharomyces cerevisiae genome.

    Geneprediction related sites
  • MAR-Finder deduces the presence of matrix association regions (MARs).
  • Additional collections of genefinding links can be found at Stanford University,
 

 
Resources for Microarray Analysis:
 

 
Resources for Protein Analysis:
  • Expasy, server for many proteinanalysis tools.
  • MASCOT for peptide mass identification .
  • Protinfo Structure/Function prediction servers.
  • Prospector at the University of San Francisco.
  • Jena Library of biol. Macromolecules, Protein and nucleic acid structures .
  • PROF secondary protein structure prediction.
  • PSORT for protein localisation.
  • ChloroP for chloroplast transition proteins and other tools, TMHMM.
  • GOR I/II/IV protein secondary prediction, several other tools.
  • NPS Network protein sequence analysis.
  • PRINTS, protein fingerprint database.
  • PFAM, a database of multiple alignments of protein domains.
  • PROSITE, a database of protein domains.
  • BLOCKS, a database of aligned protein segments.
  • PRODOM, the protein domain database.
  • INTERPRO, combination of several protein domain databases.
  • JPRED3, consensus secondary structure prediction.
  • Threader, fold class prediction.
  • SWISS-MODEL , protein homology modelling.
  • Geno3D , protein homology modelling.
  • WHAT IF - Protein modelling and visualization.
  • Rasmol,Chime,Protein Explorer - 3D protein visualization.
  • COMBOSA3D - coloring based on sequence alignment with PDB.