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Home » 2011 » August » 11 » DNA Sequence Analysis Tools
5:10 PM
DNA Sequence Analysis Tools

DNA sequence analysis tools
  1. Restriction; Detect repeats and unusual patterns
    • Restrictionmapper
    • Webcutter (Restriction analysis)
    • RepeatMasker (Search interspersed repeats and low complexity sequences)
    • REPuter (Fast computation of maximal repeats in complete genomes at Bielefeld University, Germany)
    • dnadot (Find regions of similarity in two sequences and repeats within a single sequence at Colorado State University, USA)
    • Blast 2 Sequences (Compare two sequences <150 kb to trace repeat sequences)
    • LALIGN (Finds multiple matching subsegments in two sequences at EMBnet, Swiss node)
  2. Align sequences
    • Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
    • MAP (Multiple alignment of (long) sequences without penalizing large gaps)
    • ClustalW (at EBI, UK)
    • Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
    • AMAS (Analyze multiple aligned sequences at Oxford University, UK)
    • CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)
  3. Find genes
    • Sixframe (Translate DNA sequence in all 6 possible frames at Baylor College of Medecine, USA)
    • ORF Finder (at NCBI)
    • GeneMark (Species-specific search for genes at Georgia Institute of Technology , USA)
    • GeneMark (Species-specific search for genes cfr. WebGeneMark at EBI, UK)
    • GenLang (Exon recognition at University of Pennsylvania, USA).
    • GeneMachine (Integrated comparative and predictive gene identification at NHGRI, USA)
    • NetPlantGene (Prediction of splice sites in Arabidopsis at CBS, Denmark)
    • AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)
  4. Find transcriptional elements
  5. Find tRNA
    • tRNAscan-SE
       (Search for tRNA genes in genomic sequence at Washington University, St Louis, US)
    • FAStRNA (Predict potential tRNA genes in genomic sequences at Institut Pasteur, Paris, Fr)
  6. Other tools
      • CountCodon
         (Analyse codon usage in protein coding sequence at Kazuasa DNA Research Institute, Jp)
      • MAR-Wiz
         (Search for matrix association regions at NCGR, Santa Fe, USA)
      • Reverse Complement
         (Convert DNA sequence data to it's Reverse Complement.)
      • DNA folding server
         (Fold secondary structures)
      • PRIDE
         (Primer design at DFKZ, Heidelberg, Germany)
      • Netprimer
         (Free online primer analysis at Premier Biosoft Int., Ca, USA)
      • PCR primer selection
      • Primer3
         (PCR primer selection tool at Whitehead Institute for Biomedical Research, US)
      • GeneFisher
         (Interactive PCR primer design tool at the University of Bielefeld, Germany)
      • CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer design at the Weizmann Institute, Israel)

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