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National Center for Biotechnology Information (NCBI)

Baylor Colleage of Medicine Search Launcher

The Sanger Centre

EBI-European Bioinfromatic Institute, EMBL Oustation

ExPASy

The following tables are widely used web sites for analyzing DNA, RNA, and protein sequences, as well as databases and searches for DNA, RNA, and protein structure and function.

• Major sequence databases
  • GenBank at the National Center of Biotechnology Information (NCBI)
  • European Molecular Biology Laboratory (EMBL)
  • DNA DataBank of Japan (DDBJ)
  • Protein International Resource (PIR) database
  • The SwissProt protein sequence database
  • The Sequence Retrieval System (SRS) at the European Bioinformatics Institute
• Web sites for alignment of sequence pairs
  • Bayes block aligner
  • BCM Search Launcher: Pairwise sequence alignment
  • SIMMLocal similarity program for finding alternative alignments
  • Global alignment programs (GAP, NAP)
  • FASTA program suite
  • BLAST 2 sequence alignment (BLASTN, BLASTP)
  • Likelihood-weighted sequence alignment (lwa)
• Web sites and program sources for multiple sequence alignment
  • Global alignments including progressive
    • CLUSTALW or CLUSTALX (latter has graphical interface)
    • MSA
    • PRALINE
  • Iterative and other methods
    • DIALIGN segment
    • MultAlin
    • Parallel PRRN progressive global alignment
    • SAGA genetic algorithm
  • Local alignments of proteins
    • Aligned Segment Statistical Evaluation Tool (Asset)
    • BLOCKS Web site
    • eMOTIF Web server
    • GIBBS, the Gibbs sampler statistical method
    • HMMER hidden Markov model software
    • HMMER hidden Markov model software
    • MACAW, a workbench for multiple alignment construction and analysis
    • Profile analysis at UCSD
    • SAM hidden Markov model Web site
• RNA databases and RNA analysis Web sites
  • 5S Ribosomal RNA data bank
  • Comparative RNA Web site
  • GenLang linguistic sequence analyzer
  • Gobase for mitochondrial sequences
  • Intron analysissSaccharomyces cerevisiae
  • tRNA genes, higher plant mitochondria
  • MFOLD minimum energy RNA configuration
  • Nucleic acid database and structure resource
  • Pseudobaseepseudoknot database maintained by E. van Batenburg, Leiden University
  • Ribonuclease P database Web site
  • Ribosomal RNA database project (RDP II)
  • Ribosomal RNA mutation databases
  • RiboWeb Projectt3D models of E. coli 30S ribosomal subunit and 16s rRNA
  • RNA aptamer sequence database (University of Texas)
  • RNA editing Web site, UCLA
  • RNA editing, uridine insertion/deletion
  • RNA modification database
  • RNA secondary structures, Group I introns, 16S rRNA, 23S rRNA
• Web resources for performing database searches with a simple query sequence
  • BLASTTBasic Local Alignment Search Tool
  • WU-BLAST
  • FASTA
  • BCM Search Launcher (Baylor College of Medicine)
  • TIGR gene indices search
• Phylogenetic relationships among organisms
  • Entrez: taxonomically related structures or group of organisms
  • RDP (Ribosomal database project): ribosomal RNA-derived trees
  • Tree of life: information about phylogeny and biodiversity
• Types of database searches for proteins
  • FASTA (TFASTA), SSEARCH
  • BLASTP (TBLASTN)
  • WU-BLAST
  • PROFILESEARCH
  • MAST
  • PSI- BLAST
  • INTERPRO
  • PFAM
  • CDD/IMPALA
• Web sites for performing a database search based on the Smith-Waterman dynamic programming algorithm
  • Baylor College of Medicine
  • Bic server European Bioinformatics Institute
  • National Institute of Agrobiological Resources, Tsukuba, Japan
  • G.Barton, European Bioinformatics Institute
  • DNA Databank of Japan
  • Phil Green, University of Washington
• Programs and Web sites for database similarity searches with a regular expression, motif, block, or profile
  • Regular Expression and Motifs
    • EMOTIF Scan: SwissProt and Genpept
    • Prosite patterns: SwissProt and TrEMBL
    • ISREC pattern-finding service: SwissProt and non-redundant EMBL database
    • fpat: PDB SwissProt Genpept
    • PHI-BLAST: BLAST databases
    • MOTIF: SwissProt, PDB, PIR, PRF, Genes
  • Blocks
    • BLOCKS
    • MAST
    • BLIMPS
    • Probe
    • Genefind
  • Profiles
    • Profilesearch
    • Profile-SS
• Programs and Web pages for sequence translation and related information
  • Arabidopis intron splice site table
  • Codon usage database
  • Ecoparse for finding E. coli genes based on HMM model
  • EST-GENOME for alignment of EST/cDNA and genomic
  • Exon recognizer, including GeneScope
  • FGENES and related programs that use linear discriminant analysis or hidden Markov models
  • FINEXXexon intron boundary analysis
  • GeneFinder access site at the Sanger Center
  • Genehacker for microbial genomes based on HMMs
  • GeneID-3 Web server using rule-based models, and GeneID+
  • GeneMark and GeneMark.hmm uses hidden Markov models
  • GeneParsera Web page, uses combination of neural network and dynamic programming methods
  • Genescan using Fourier transform of DNA sequences to find characteristic patterns
  • GeneScope
  • Genie for finding human genes in 10-kb DNAs and in Drosophila by hidden Markov models and neural networks
  • Genetic code variations
  • GenLang using linguistic methods
  • GenScan based on probabilistic model of gene structure for vertebrate, Drosophila, and plant genes
  • Genseqer for aligning genomic and EST sequences
  • Glimmer uses interpolated Markov models for prokaryotic translation
  • GrailII prediction by neural networks based on scores of characteristic sequence patterns and composition
  • Human splice sites with decision tree analysis
  • INFO for finding splice junctions by database similarity search
  • INFOGENE: a database of known gene structures and predicted genes
  • Initiation codon analysis
  • Microbial genome coding region identification based on Markov chains of order 5
  • MZEF uses quadratic discriminant analysis for human, mouse, Arabidopsis, and S. pombe exons
  • NetGene uses neural networks for analysis of splice sites in human, C. elegans, and Arabidopsis genes
  • NetPlantGene
  • NetStart uses neural networks for gene prediction in vertebrate and Arabidopsis genes
  • Procrustes based on comparison of related genomic sequences
  • Push-button Gene Finder for gene identification using Markov and hidden Markov models
  • SplicePredictor for plants uses trained logitlinear models
  • Splicing Sites by neural network at LBNL
  • Translate tool at ExPASy
  • Translation machine on the Web at EBI
  • Translation of large genome sequences on the Web
  • Webgene, a set of gene prediction tools and concurrent database similarity searches
  • Webgenemark and Webgenemark.hmm
  • Yeast splice sites by M. Ares Jr. laboratory
• Promoter prediction programs, Web pages, and related information
  • ConsInspector
  • Core-Promoter–for finding RNAPII promoters of human genes by quadratic discriminant analysis
  • EPD Eukaryotic promoter database
  • EpoDB genes expressed during vertebrate erythropoiesis
  • FastM for transcription factor binding sites
  • GeneExpress analysis of transcriptional regulations with TRRD database
  • Genome inspector for combined analysis of multiple signals in genomes
  • GrailII prediction of TSS by neural networks based on scores of characteristic sequence patterns and composition
  • MAR-FINDER for finding matrix attachment regions
  • MatInspector
  • Nuclear (including glucocorticoid) receptor resource
  • Mirage (Molecular Informatics Resource for the Analysis of Gene Expression)
  • NNPP Promoter Prediction by Neural Network for prokaryotes or eukaryotes
  • NSITE–search for TF binding sites or other consensus regulatory sequences
  • PLACE plant cis-acting regulatory elements
  • PlantCARE plants cis-acting regulatory elements
  • Pol3scan for RNAP III/tRNA promoter sequences using pattern scoring matrices
  • Polyadq for locating polyadenylation sites
  • Promoter element weight matrices and HMMs
  • Promoter II for recognition of PolII sequences by neural networks
  • PromoterScan
  • RegScan for promoter classification
  • Sequence walkers for graphical viewing of the interaction of regulatory protein with DNA binding site
  • Signal scan for transcriptional elements
  • TargetFinder for promoter searching in selected annotated sequences
  • TESS for searching for transcription factor binding sites
  • Tfbind for transcription factor binding sites
  • Thyroid receptor resource
  • Transfac programs providing search for TF binding sites. MatInd for making scoring matrices and MatInspector for searching for matches to matrices
  • TSSG, like TSSW but based on sequences from a different promoter database
  • TSSW; recognition of human PolII promoter region and start of transcription by linear discriminant function analysis
  • Yeast cell cycle gene retrieval and promoter analysis
  • Yeast cell cycle analysis project
• Main Web sites for protein structural analysis
  • Protein data bank (PDB)
  • National Center for Biotechnology Information Structure Group
  • Structural Classification of Proteins at Cambridge University
  • Biomolecular Structure and Modelling group at the University College, London
  • European Bioinformatics Institute, Hinxton, Cambridge
  • Swiss Institute of Bioinformatics, Geneva
  • The PredictProtein server at the European Molecular Biology Laboratory at Heidelberg, Germany
• Programs for viewing protein molecules
  • Chime
  • Cn3d
  • Mage
  • Rasmol
  • Swiss 3D viewer, Spdbv
• Selected programs for performing protein secondary structure prediction
  • Baylor College of Medicine (BCM)
  • DSC
  • J-Pred structure prediction server
  • NNPRED
  • NPS@ server, MLR combination for secondary structure prediction
  • Protein Sequence Analysis (PSA) System
  • PREDATOR
  • PSSP
  • Simpa96, SOPM, SOPMA
  • SSP
  • UCLA-DOE structure prediction server
• Threading servers and program sources
  • 123D
  • 3D-PSSM
  • Honig lab
  • Libra I
  • NCBI structure site
  • Profit
  • Threader 2
  • TOPITS
  • UCLA-DOE structure prediction server
• Web sites for predicting structural features of a query sequence
  • Modeller
  • Swiss-model
  • Whatif
• Web resources and references for genome information and analysis
  • Prokaryotic genomes
    • MAGPIE: Multipurpose Automated Genome Project Investigation Environment
    • Microbial genome databases
    • Microbial genome databases another site
    • Comparative genome analysis in P. Bork laboratory
    • TIGR: The Comprehensive Microbial Resource Home Page-the omniome
    • U.S. Dept. of Energy Joint Genome Initiative
  • Genomic databases of model organisms and other genome databases
    • Arabidopsis thaliana genome displayer
    • A. thaliana information resource TAIR
    • Caenorhabditis elegans (worm) database
    • C. elegans chromosomes
    • C. elegans genome project
    • C. elegans proteome database I
    • C. elegans proteome database II
    • Dictyostelium discoideum genome information
    • Drosophila melanogaster Berkeley Drosophila genome project
    • D. melanogaster chromosomes
    • D. melanogaster: Flybase, a genomic database
    • E. coli genome project
    • E. coli genome and proteome database GenProtEC
    • E. coli index
    • Genome databases at NCBI
    • Genome databases other than NCBI
    • Genome list at NIH
    • Mitochondrial DNA Database MitBASE
    • Mouse (Mus musculus) genome informatics
    • Plant genome projects
    • Organelle genome sequences
    • Parasite genome databases and genome research resources
    • Retroviral genotyping and analysis site
    • Rice (Oryza sativa) genome project
    • Saccharomyces cerevisiae: View of 16 chromosomes
    • S. cerevisiae, YPD Yeast Proteome database, a commercial database
    • S. cerevisiae (budding yeast) database SGD
  • Human and mouse genome comparisons
    • Celera Genomics
    • Comparison of human (Homo sapiens) and mouse (M. musculus) chromosomes
    • Cooperative Human Linkage Center: mouse-clickable map of chromosomes
    • Draft Human Genome Browser
    • Human sequence polymorphisms, mutations, and mapping
    • Human EST project
    • Human genome resources at NCBI
    • Mouse (M. musculus) chromosomes: mouse-clickable map
    • On-line inheritance in man: Johns Hopkins University and NCBI
    • Whitehead Institute for Biomedical Research
  • Gene and genome relationships and proteome analysis
    • Alfresco: Visualization tool for genome comparison
    • allgenes.org: A comprehensive gene index (catalog) derived from ESTs and predicted genes
    • CGAP: Cancer genome anatomy project
    • COG (cluster of orthologous groups): A gene classification system
    • DOGS: Database of genome sizes
    • E-CELL: A modeling and simulation environment for biochemical and genetic processes
    • FAST_PAN for automatic searches of online EST databases to identify new family members (paralogs)
    • GeneCensus Genome Comparisons by encoded protein structures
    • GeneQuiz: An integrated system for large-scale biological sequence analysis and data management
    • Genes and disease: Map location on human chromosomes
    • Genome channel at Oak Ridge National Laboratories
    • GOLD?: Genomes OnLine Database
    • IMGT ImMunoGeneTics Database specializing in Immunoglobulins, T-cell receptors, and Major Histocompatibility Complex (MHC) of all vertebrate species
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • MIA Molecular Information Agent: A Web server that searches biological databases for information on a macromolecule
    • Orthologous gene alignments at TIGR
    • STRING Search Tool for Recurring Instances of Neighboring Genes
    • Taxonomy browser at the NCBI arranges genomes taxonomically for sequence retrieval
    • UniGene System gene-oriented clusters of GenBank sequences useful for gene identification
    • U.S. Dept. of Agriculture, Agricultural Research Service reference site for plant and animal genomes
  • Metabolism and regulation, functional genomics
    • 2D gel analysis of proteins: List of organisms
    • AlignAce for promoter analysis of coordinately regulated genes, e.g., microarrays by Gibbs sampling
    • ArrayExpress database at European Bioinformatics Institute for microarray analysis
    • BRITE: Database of protein-protein interactions and cross-reference links
    • Ecocyc electronic encyclopedia of genes and metabolism of E. coli
    • EpoDBis: A database of genes that relate to vertebrate red blood cells
    • Expression Profiler tools for analysis and clustering of gene expression and sequence data
    • Functional genomics sites
    • GeneCensus Genome Comparisons by encoded protein structures
    • GENECLUSTER
    • GeneX: A Collaborative Internet Database and Toolset for Gene Expression Data
    • MetaCyc metabolic encyclopedia (see EcoCyc)
    • Microarray guide
    • Microarray project at NIH
    • Microarray software
    • microarrays.org: A new public source for microarraying information, tools, and protocols
    • SMART: For the study of genetically mobile protein domains
    • SWISS-2DPAGE: Two-dimensional polyacrylamide gel electrophoresis database
    • TIGR: Annotation and gene indexing resources, including analysis of the transcribed sequences represented in the public EST databases.
    • WIT (What is there?): Interactive metabolic reconstruction on the Web
    • Yeast (S. cerevisiae) transcriptome
    • Yeast genome (S. cerevisiae) on a chip
  • Gene nomenclature, functional characterization, and genome database development
    • A. thaliana nomenclature
    • Genome Annotation and Information Analysis GAIA
    • GeneQuiz: An integrated system for large-scale biological sequence analysis and data management
    • GFF (Gene-Finding Features): Specification for describing genes and other features of genomics
    • GO (gene ontology) controlled vocabulary
    • K2 system for support of distributed heterogeneous database and information resource integration
    • Kleisli Project: A tool for broad-scale integration of databanks across the Internet
    • MAGPIE: Multipurpose Automated Genome Project Investigation Environment
    • Mendel Plant Gene Nomenclature Database
    • RefSeq and LocusLink: A curated set of reference sequences with map locations, a foundation for functional annotation of the human genome
    • TAMBIS: A conceptual model of molecular biology and bioinformatics and methods for querying the model