O
WWU Münster UKM
IoB
NEWS
2017-09-05
Juan Manuel Galvez, welcome to our institute!
2017-09-05
Julian-Hendrik Matschke, welcome to our institute!
2017-07-11
Congratulations Philipp Fervers for for the successful defense of his doctoral thesis.
2017-07-24
Yukie Kashima, welcome to our institute!
2017-07-11
"Inferring clonal structure in HTLV-1-infected individuals: towards bridging the gap between analysis and visualization” by Farmanbar et al. has bee published by Human Genomics.
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2017-07-03
Welcome Reza Halabian, our new PhD student..
2017-06-27
"Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer” by Suzuki et al. has bee published by DNA Research.
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2017-06-14
"Serotyping dengue virus with isothermal amplification and a portable sequencer.” by Yamagishi at al. has been published by Scientific Reports.
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Main Databases

  • PubMed - abstracts for 11 million biomedical articles
  • Entrez - gateway to nucleotide and protein sequences
  • LocusLink - curated sequence and gene descriptions
  • PDB - 3D protein database at RCSB
  • SwissProt - keyword search annotated protein collection
  • SRS - query Swiss sequence retrieval system
  • EBI SRS - query session at EBI sequence retrieval center
  • EMBL - gateway to EMBL sequence and structure databases
  • Hovergen - homologous vertebrate genes database
  • HUGE - unidentified human proteins in KIAA series
  • MIPS - gateway to protein information center in Munich
  • OWL - non-redundant protein sequence database
  • PIR - gateway to PIR protein database and query tools
  • ChromList - lists UniGene clusters by chromosome
  • ChromProt - lists human proteins by chromosome
  • KEGG - Kyoto encyclopedia of pathways and maps
  • Taxonomy - taxonomic classes at NCBI
  • TreeLife - tree of life taxonomy project
  • Hugo - recommended gene symbols at Genew3
  • OMIM 1 and 2 - simple and complex searches at OMIM
  • Marshfield - genetic and physical maps at Marshfield
  • HGMD Mut - human gene mutation database at Cardiff
  • LocMutations - locus-specific mutation databases
  • Mitomap - human mitochondrial genome database
  • Mito - mitochondrial genomes and alignment
  • MitoWustl - mitochondrial genes, mutations and disorders
  • MitoP - mitochondrial genes, proteins and diseases at Munich
  • MitoDat - nuclear genes specifying mitochondrial biogenesis
  • UDB - integrated human genome map
  • UniGene - query UniGene
  • UniGene HIB - annotated Unigene clusters and blast service
  • Contigs - search NT contigs, dbSTS, GenMap99
  • Marker - search for marker, YACs, contigs
  • SNP - single nucleotide polymorphisms at SNP Consortium
  • dbSNP - search for single nucleotide polymorphisms at NCBI
  • BodyMap - database of human and mouse gene expression
  • TransTerm - sequence context of stop and start codons
  • ESTScan - detects coding regions despite frameshifts and low quality
  • RegulonDB - transcription regulation database for various organisms
  • Rebase - restriction enzyme cleavage sites
  • SpliceDB - canonical and non-canonical splice sites in mammals
  • MemTrans - genomic comparisons of membrane transport systems
  • Geneimprint - imprinted gene database
  • Codon - codon usage database

Genome Browsers & "Complete" Genomes

  • Genome Browser - human genome assembly and track browser at UCSC
  • Ensembl - human genome and disease gene browser at EBI/Sanger
  • Map Viewer - human genome assembly and map viewer at NCBI
  • Genome - query human genome and annotation database tables
  • Download - download human genome and install mirror
  • euGenes - five species map browser and 37,049 human gene reports
  • Vista - visualization tool for long genomic alignments
  • TIGR CMR - comprehensive microbial resource and genome browser
  • NCBI - human and animal genome projects at NCBI
  • Sanger - human genome project at Sanger Centre
  • Jax - mouse genomics at Jackson Laboratory
  • RatMap - rat genome database at Goteborg
  • Zfin - zebrafish information network and database project
  • Exofish - genome analysis of Tetraodon nigroviridis
  • Flybase - database of drosophila genomics at Indiana
  • BDGP - fruit fly genomics center at Berkeley
  • WormBase - nematode mapping, sequencing and phenotypic repository
  • ACeDB - genetics and genomics resource launcher
  • SGD - yeast genome database
  • TAIR - the arabidopsis information resource and tool center
  • TIGR db - bacterial genomes at TIGR
  • GOLD - monitors genome projects world-wide
  • GenTotals - monitoring tables for genome progress

Gene Prediction and Feature Finding

  • Mesquite: A modular system for evolutionary analysis
  • Genscan D and M - identification of complete gene structures in genomic DNA
  • GenomeScan - predicts genes incorporating protein homology
  • RGD - comparative mapping tool for rat-mouse-humany synteny
  • FGENEH - splice sites, coding exons, gene models, promotor and polyA
  • Softberry - nucleotide sequence analysis, genes, promoters
  • TwinScan - gene prediction for eukaryotic genomic sequences
  • WebGene - ten tools for analysis of protein-coding gene structure
  • Rosetta - predicts human coding exons based on homology
  • GrailEXP - exons, genes, promoters, polyA, CpG islands at ORNL
  • GeneWise2 - compares protein to genomic with introns and frameshifts
  • Genie - finds multi-exon genes only, trained on human
  • AAT - analysis and annotation tool for finding genes
  • HMMgene - prediction of vertebrate and nematode genes
  • NetGene2 - neural network predictions of splice sites
  • GeneMark - gene prediction server at EBI
  • GeneID - gene prediction of selected signals and exons
  • RNAGenie - locates RNA genes from secondary structures
  • Vienna RNA - seven RNA analysis tools
  • Reverse Comp - reverse complement of DNA sequence
  • McPromoter - finds eukaryotic RNA polymerase II transcription starts
  • PromoterScan - predicts promoters using homologies with Pol II promoters
  • ORF Finder - open reading frame finder for ORFs of cutoff size
  • SeqTrans - identifies open reading frames in finished genomic
  • Emboss - predict CpG islands and isochores
  • UTR - untranslated regions of eukaryotic mRNAs
  • AltSplice - database of alternate splicing in Ests and disease genes
  • Webcutter - finds restriction endonuclease sites
  • FSED - frameshift error detection in new sequences
  • CheckSeq - uses homology to find coding regions and sequence errors
  • ERR_WISE - detection of frameshift sequencing errors
  • SEQERR - detection of frameshift error in coding regions
  • MutCheck - transcription and translation effect of mutations
  • Sift - predicts tolerated and untolerated protein substitutions
  • TransFac - transcription factor database and tool collection
  • MatInspector - searches for transcription factor binding sites
  • VarSplice - collection of annotated splice variants
  • TransPath - pathways in regulation of transcription factors
  • TfScan - scans DNA sequences for transcription factors
  • RepeatMasker - finds retroposons and repeats
  • Censor - finds repeated elements, Repbase updates, maps
  • Tandem - tandem repeat finder in DNA
  • DotPlot - dot plot for internal DNA sequence repeats
  • PatternHunter - finds approximate repeat patterns in genomic DNA
  • TandemRepeats - finds adjacent imperfect repeat patterns in DNA
  • Dst - finds human repeats and separated self-homology
  • REPuter - genomic repeats of all types to 100kbp
  • Tinoco - suggests secondary structure in RNA or DNA
  • RNA_align - aligns two RNA species from secondary and tertiary structures
  • REP - searches proteins for internal repeats
  • Radar - detects and aligns protein repeats
  • Repro - recognises repeats in a single protein query

Protein Tools and Browsers

  • SwissTools - large collection of protein tools and databases
  • Translate - translates DNA into 6 frames
  • ReverseTrans 1 and 2 - reverse-translates protein into DNA
  • SAPS - statistical analysis of protein sequences
  • Emboss - peptide information and statistics
  • Signalp - predicts signal peptide cleavage sites
  • Psort - protein sorting signals
  • TMpred - predicts transmembrane segments and orientation
  • TMHMM - predicts transmembrane helices
  • TopPred2 - topological prediction of membrane proteins
  • TMAP - predicts membrane proteins from multiple alignment
  • COILS 1 and 2 - prediction of coiled-coil regions in proteins
  • PREDATOR - secondary structure from multiple sequences
  • SSCP - predicts helix, strand and coil from composition
  • STRIDE - secondary structure from atomic coordinates
  • BCM SS - secondary structure by four methods
  • Jpred - consensus method for secondary structure prediction
  • TOPS - protein topology atlas and tool collection
  • Interpro - integrated resource of protein families, domains and sites
  • Pfam - alignments and hidden Markov models of protein domains
  • SMART - simple modular architecture research tool
  • ProDom - protein domain database
  • ScanProsite - scans a sequence against PROSITE
  • ProfileScan - scans sequence against profile databases
  • FingerPRINTScan - search tool for Prints motifs
  • ppsearch - pattern search tool for DNA or protein motifs
  • HMMER - profile hidden Markov models for sequence analysis
  • SAM - sequence alignment and modelling system by HMM
  • BLOCKS - aligns ungapped segments of conserved protein regions
  • IMPALA - blast search of BLOCKS conserved protein regions
  • Blimps - improved BLOCKS search tool
  • Motif - searches for motifs in query sequence
  • FPS - family pairwise search library of protein families
  • Cognitor - compare sequence to clusters of orthologous proteins
  • Scop - structural classification of proteins
  • SuperFamily - genomewide structural classification of proteins
  • Pratt - search for conserved patterns in protein sequences
  • Cath - hierarchical classification of protein domain structures
  • MAST - motif alignment search tool
  • MEME - analyzes protein and DNA for motifs
  • Profam - curated protein classification and homology domains
  • TIGRFAMs - protein families based on hidden Markov models
  • ProtClass - protein classification browser
  • Argos - protein surface and secondary structure tools
  • Dali - coordinates of query compared to PDB database
  • 123D - predicts tertiary structure
  • 3Dee - database of protein domain definitions
  • FSSP - fold classification based on structure
  • PredProt - predicts protein structure
  • PredictProt - threading, secondary, solvent and transmembrane
  • Fold - 3D structures based on homologous sequences
  • MaxSprout - protein backbone and side chains from alpha coordinates
  • CE - finds structural alignments from PDB
  • PQS - protein quaternary structure query form at EBI
  • DIP - database of interacting proteins
  • ProtFam - average core structures for families from structure
  • SCWRL - sidechain placement using a rotamer library
  • ASC - analytic surface calculation package
  • AA Contacts - residue contacts, solvent accessibility
  • ProStar - protein potential site
  • Sweet - constructs 3D models of oligosaccharides from formula
  • GlycoSuiteDB - curated relational database of glycan structures
  • SwissPdbView - deep view for manipulation and analysis of PDB structures
  • PBD Viewers - choices of plug-ins and 3D structure viewers
  • Kinemages - interactive 3D protein web display
  • RasMol - molecular visualization resource
  • ProtExplorer - macromolecular viewer related to RasMol
  • Chime - interactive web plug-in for 3D molecular structures
  • Morph - downloadable protein shape morpher
  • COMBOSA3D - combines alignment, protein 3D, and Chime to color
  • Boxshade - pretty shading of multiple alignments
  • ProtCol - tool for coloring proteins, default is by hydrophobicity
  • ProtExpl - protein explorer interactive software

Family Specific

  • GPCRDB - G-protein coupled receptor database
  • NucleaRDB - nuclear receptors at UCSF
  • NRR1 - nuclear receptor resource at Georgetown
  • HORDE - human olfactory receptor genes
  • GPCR - classifies G-protein coupled recepters
  • Secator - classifies any protein family (receptors, tRNA synthetases)
  • Merops - curated database on proteases
  • Prion - annotated prion-doppel gene family

Blast, Blat, and Align Sequences

  • Blast - java-free NCBI blast launch
  • Swiss - blastp and tBlastn HTGS, UniGene at EMBnet
  • Blast2 - restricts blast to user query and target
  • BlastU - blast query against user fasta database
  • Batch - batch blast from Baylor
  • Blat - quick alignment of query to human genome assembly
  • HumFin - blast finished human genome chromosome
  • Mus 1 and 2 - blast finished mouse genome by chromosome
  • Ensembl - blast human genome project
  • Sanger - blast sequencing center chromosomes
  • Traces - blast against raw new genomic trace reads
  • SSAHA - trace server at Ensembl
  • Hunt - search human novel transcript cDNAs
  • WABA - genomic to genomic comparisons
  • Pipmaker - percent identity plot alignment of two genomic sequences
  • DBA - aligns two sequences sharing conserved blocks
  • Alfresco - comparative genome sequence analysis
  • ClustalW - aligns multiple sequences
  • MAlign - aligns multiple sequences with flexible formatting
  • Lalign - find multiple matching subsegments in two sequences
  • Consensus - calculates consensus to ClustalW alginment
  • Fasta3 - fasta3 alignment of protein sequence
  • SnpFasta3 - alignment to HgBase SNP consortium
  • MPsrch - alignment tool with many parameter controls
  • Scanps - multi-alignment of query protein sequence

Tools Collections

  • NHGRI and EBI and NCBI --"Genome Hub" pages
  • NCBI - site map to extensive services
  • BCM - launches numerous nucleotide and protein tools
  • CMS - extensive directory of tools by category
  • ABI - very large French tool compilation
  • NAR - curated tool collection at Nucleic Acid Research
  • UCSD - genome analysis by task area
  • Workbench - unified area for searching and analysis
  • EMBL1 - collection of database searching and tools
  • EMBL2 - various EMBL alignment tools
  • UCSF1 and 2 collections of tool links at UCSF
  • MDC - bioinformatics tools at Delbruck Center
  • EBI - tool and utility collection at EBI
  • SDSC - tools at San Diego Supercomputer Center
  • Bork - ten tool server of Bork lab
  • Biocatalog - bioinformatic software collection
  • MIA - search agent finds macromolecular information
  • Phylip - tools and software for phylogenies
  • Phylo - provides 14 utilties for phylogenetic analysis
  • PAML - maximum likelihood of evolutionary parameters and hylogenies
  • Stothard - The Sequence Manipulation Suite

Journals, Alerts, and General Internet

  • PubMedJB - journal browser allows access to current issues
  • Pubcrawler - provides alerts to new abstracts at PubMed
  • HiWire - publishes online journals and provides alerts
  • SeqAlert - provides daily homology sequence alerting
  • New Issues - provides entry to 35 genomics jounals
  • GenomeBio - free access to post-genomics journal, pre-print server
  • PNAS - free access to month-old articles in PNAS
  • JBC - nearly free access to most cited journal
  • Science - high circulation general science journal
  • Nature - gateway to restricted spin-off journals
  • AmJHumGen - leading disease gene annotation journal
  • Genomics - genomics articles sometimes stale
  • GenomeRes - genomic research and methods articles
  • Pedro - large journal (and tool) collection
  • Web of Science - ISI web of knowledge
  • OMD - online medical dictionary
  • Google - best internet search site for web tools
  • Lycos - widely used general search tool
  • Yahoo - internet categories and news
  • Nando - science and health news feed
  • LangTrans - useful for rough translations between languages
2017-10-11 11:08