Nucleic acid sequence analysis

• READSEQ : sequence format conversion
• Reversion, complementation
• Composition - Codon usage
• PCR - Primer selection
• Prediction of gene structure - ORFs
• Translation - Coding regions
• Restriction maps
• Search for specific sites
• Search for motifs and repetitions
• Comparison with another sequence or with a sequence database
• Identification by restriction pattern comparison
• Prediction of secondary structure
• Multiservices servers
• Mail servers

Reversion - Complementation

• Reverse Complement (Sequences utilities : sequence format conversion (Readseq), filter repeats (RepMask), PCR primer selection, reversion-complementation of a nucleic acid sequence (Reverse Complement), translation in 6 frames (6 Frame Translation), restriction maps (WebCutter) (BCM)

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Composition - Codon usage

• CUTG : Codon Usage Tabulated from GenBank by organism (Japon)
• Countcodon program : compilation a sequence into a codon usage table. (Japon)
• DNA Fragment Length Estimation Predictor : alculate the size of DNA fragment in an agarose gel from their molecular weight and their distance (IBC)
• COA (Correspondence Analysis) : COA is suited for studying differenciation among codons or for examining trends in amino-acids composition. For instance, it is possible to use COA to detect highly expressed genes in unicellular organisms (e.g., bacteria, yeast), or in some simple multicellular organisms (e.g, nematod, fruitfly). See also information about NetMul (multivariate analysis system) (University of Lyon)
• The RNA Modification Database : provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA. (Universite de l'UTAH)

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PCR - Primer selection

• [Technology and protocols]
• Analysis :
  • Primer Selection : xprimer version Text or xprimer version Image provides an interface to a PCR primer selection program. [Information] (Alces)
  • PCR Primer selection This program was designed for selection of PCR primers to amplify precise regions from relatively low complexity genomes. (Alces)
  • STS Pipeline : This tool is used for automated analysis and STS primer picking of short DNA sequences : duplicate checking, simple sequence repeat finding, vector identification, BLAST searching, and the actual primer picking itself. The pipeline is composed of multiple small programs, which can be individually configured and linked together, to suit different laboratory needs. (WITCGR-MIT, Minnesota)
  • GeneFisher : Interactive Primer Design [Information] (University of Bielefeld, Germany)
  • Primer (WITCGR-MIT, Minnesota)
  • Primer (BRUS, Singapour)
  • Web Primer : DNA and Purpose Entry (SGD, Stanford, US)
  • World Wide Web Primers (Williamstone Enterprises) :
    • Primers! for the WWW (no java application)
    • Primers! for the WWW (java application)
• Physico-chemical characterization :
  • Oligonucleotide Vital Statistics : composition, PM, TM, DO of an oligonucleotide. (Cambridge)
  • Oligo Calculator : calcul of PM, TM, %GC (EMBL)
  • POLAND : profile of thermal denaturation. (Dusseldorf)
  • Oligonucleotide Tm Determination (Alces)
  • Primer Calculator (Williamstone Enterprises)

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Prediction of gene structure - Coding regions

• BCM Search Launcher (proposes different methods) :
  • BCM Gene Finder : search for potential splicing sites, exons, recognition of promoters region and start of transcription (via e-mail ou WWW)
  • Gene feature searches (via e-mail ou WWW)
• Search for Structural Patterns (via e-mail) : E-Mail server for analysis of uncharacterized sequences. (Weizmann Institute)
• EcoParse : gene search in E. coli DNA by the "Hidden Markov Model" (A. Krogh, I. S. Mian and D. Haussler) (via e-mail)
• NetGene : prediction of splice sites in vertebrate genes. (CBS, Danemark)
• NetPlantGene : prediction of splice sites Arabidopsis thaliana genes. (CBS, Danemark)
• FINDORF : open frame analysis. (CRIBI, Italie)
• ORF Finder : graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database. (NCBI)
• FSED (FrameShift Error Detection) : is suited to the analysis of newly determinated sequences before their submission to the databases, the potential frameshift errors being readily resolved by examination of raw data such as gel readings. (CNRS, Marseille)
• GENIE (A Gene Finder Based on Generalized Hidden Markov Models). Adapted for human genes and other vertebrate sequences. Not guaranteed to work well on non-vertebrates. (University of California et LBNL, USA)
• GRAIL : prediction of potential coding regions. (ORNL, Oak Ridge National Laboratory, US)
• RecSta : prediction of coding regions (CDS or exons) in the 3 sequence frames from codon usage. (University of Lyon).
• The Exon/Gene Search Engine
• Splice Site Prediction by Neural Network (LBNL).
• PROCRUSTES WWW Server : identifies genes based on the Spliced Alignment algorithm, which explores all possible exon assemblies and finds the multi-exon structure with the best fit to a related protein. (USC).
• WebGene Server (ITBA) :
  • GenView : a computing system for protein-coding gene prediction.
  • ORFGene : gene structure prediction using information on homologous protein sequence.
  • SpliceView : splicing signals prediction .
  • SpliceNet : Splicing signals prediction using neural networks.
  • HCpolya : Hamming Clustering Method for poly-A prediction in Eukaryotic Genes.
  • HCtata : Hamming Clustering Method for TATA signal prediction in Eukaryotic Genes.
  • MSA : Mutational Spectrum Analysis.
• GENMARK : The GenMark server provides a gene finding service using an algorithm based on non-homogeneous Markov chain models. The GenMark is most accurate for finding prokaryotic genes, for analyzing cDNA sequences and for finding rather long exons (more than 100bp) in eukaryotic genomic DNA (via e-mail)
• GenLang : is a syntactic pattern recognition system, which uses the tools and techniques of computational linguistics to find genes and other higher-order features in biological sequnece data. (CBIL, Pennsylvania)

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Translation

• Standard Codons for Nuclear Genes (Alces, USA).
• The different genetic codes (NYC)
• Translate tool : translation in 6 frames, each one may be submitted to SwissProt or may be data to Blast. (Expasy)
• DNA sequence translation (Alces, Minnesota)
• The Protein Machine : translation in direct frame, with colour representation (amino acid classes). (EBI)

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Restriction maps

• Rebase searching (Restriction Enzyme Database) (John Hopkins) or searching by SRS (INFOBIOGEN)
• Webcutter: on-line tool for restriction mapping nucleotide sequences (analysis with all the enzymes or with a given enzyme subset) (Texas, USA)
• WWWtacg Submission Form : restriction enzyme mapping and analysis

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Search for specific sites

• Search for potential TRANScription FACtor binding sites (TRANSFAC database, Info)
  • MatInspector is a tool that utilizes a large library of matrix descriptions for transcription factor binding sites to locate matches in sequence (GBF, Allemagne)
  • TESS Basic Query (Transcription Element Search Software) (CBIL, US)
  • TFSEARCH (ICR, Japon)
• Pol3scan : searches the eukaryotic polymerase III intragenic control regions A box and B box. (Italie)

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Search for motifs and repetitions in the nucleic acid sequence

• Search for a personal pattern :
  • Protein Motifs : search for a personal protein pattern in a nucleic acid sequence (personal sequence or entry of GenBank). (Alces)

  Search for databank motifs :

  • Web Signal Scan Service : finds and lists homologies of published signal sequences (TRANSFAC or TFD) with the input DNA sequence. (Sigscan program).
    • Egalement, à BRUS (Singapour)
  • PatternSearch : comparison of a user nucleic acid sequence with the TRANSFAC database. (GBF)
  • Web Promoter Scan Service : predicts promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences. (BIMAS)
    • à BRUS (Singapour)
  • FastM : can detect distance-correlated pairs of transcription factor binding sites from the TRANSFAC database in a nucleic acid sequence. (GSF, Germany)

  Search for alignment databank motifs :

  • Block Searcher : comparison of a personal nucleic acid sequence (translated by the program) with the BLOCKS database (multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins) or with the PRINTS database (Protein Motif Fingerprint Database Site) (FHCRC, Hutchinson).
  • Comparison of a personal nucleic acid sequence with the PRODOM database (info, homologous domains detected in SwissProt) :
    • Blast Prodom Form (WWW) (Blastx) or Blast Prodom with Graphical output or via e-mail. (INRA, Toulouse)
    • Search ProDom with BLAST (Blastx) (Sanger)
  • BLAST search in SBASE3.1 (Blastx) : comparison of a personal nucleic acid sequence with the SBASE database (info (ICGEB, Trieste)

  Repeats searching :

  • Censor Web Server : allows users to have query sequences aligned against a reference collection of human or rodent repeats. (Genetic Information Research Institute, California)

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Identification by restriction pattern comparison

• RIFLE - Rapid Identification by Fragment Length Evaluation : the RIFLE system compares restriction patterns of possibly unknown microorganisms against a database of theoretical restriction patterns generated from a 16S rDNA database, e.g. the RDP database. (BiBiServ, Université de Bielefeld, Germany)

Prediction of secondary structure

• bend.it @ Server : This server predicts bendability and propoensity to curvature rom DNA sequences. (ICGEB, Trieste, Italy)
• RNA secondary structure prediction : prediction from a sequence or from a multiple alignment (Belozersky Institute, Moscow State University).
• WWW mfold server. See Michael Zuker's RNA page. (IBC)
• RNA Folding Software for Mac or PC.

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Multiservices servers

• ALCES Home Page (Minnesota, USA)
  • VGC (Virtual Genome Center)
• BCM Search Launcher (Baylor College of Medicine, USA)
  • Sequence Utilities
  • Gene Feature Searches
  • BCM Gene Finder
• BIMAS (BioInformatics & Molecular Analysis Section, CBEL, DCRT, NIH, Bethesda, USA)
  • Accessible Analyses
• BIC (Home Page) (BioInformatics Centre, National University of Singapore)
  • BRUS (Biocomputing Resources at the University of Singapore)
• CBS (Center for Biological Sequence Analysis, The Technical University of Denmark)
  • Prediction servers
• EMBL(Home Page). (European Molecular Biology Laboratory, Heidelberg, Allemagne)
  • EMBL WWW Services
  • Java-based Molecular Biology Work Bench
• IBC (Institute for Biomedical Computing, Washington University)
  • Locally Developed Interactive Tools
• ITBA - CNR (International Centre for Genetic Engineering and Biotechnology (Trieste)
  • WebGene
  • WebMutation
  • WebData
• LBNL (Lawrence Berkeley National Laboratory Human Genome Center, Berkeley, USA)
  • LBNL Human Genome Informatics Group : Projects
  • BDGP (Berkeley Drosophila Genome Project)
• NCSA (Home Page). (University of Illinois, USA)
  • Biology Workbench
• Whitehead Institute - MIT (Cambridge, Massachusetts, USA)
  • STS Pipeline v1.2

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