BioTech FYI Center

DNA Sequence Analysis Tools

DNA Sequence Analysis Tools
Restriction, Detect repeats & unsual Patterns
  • Webcutter (Restriction analysis)
  • RepeatMasker (Search interspersed repeats and low complexity sequences)
  • dnadot (Find regions of similarity in two sequences and repeats within a single sequence at Colorado State University, USA)
  • LALIGN (Finds multiple matching subsegments in two sequences at EMBnet, Swiss node)
  • Tandem Repeats Finder (at Mount Sinai School of Medecine, NY, USA)
  • Dot Plot (Compare a large sequence with itself at Virtual Genome Center)
  • Blast 2 Sequences (Compare two sequences <150 kb to trace repeat sequences)
  • Zinfo (Detection of unusual sequences in large DNAs at Virtual Genome Center), USA)
Align Sequences
  • Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
  • ClustalW (at EBI, UK)
  • Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
  • CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)
  • MAP (Multiple alignment of (long) sequences without penalizing large gaps)
  • ClustalW (Multiple sequence alignment at WUSTL, USA)
  • ClustalW (at the Baylor College of Medicine, USA)
  • AMAS (Analyze multiple aligned sequences at Oxford University, UK)
Find Genes
  • Webtrans (Translation and codon usage of very large sequences at Virtual Genome Center)
  • GeneMark (Species-specific search for genes with WebGeneMark , WebGeneMark.hmm and Heuristic GeneMark at Georgia Institute of Technology , USA)
  • GenLang (Exon recognition at University of Pennsylvania, USA)
  • GeneMachine (Integrated comparative and predictive gene identification at NHGRI, USA)
  • AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)
  • Sixframe (Translate DNA sequence in all 6 possible frames)
  • ORF Finder (at NCBI)
  • GeneMark (Species-specific search for genes cfr. WebGeneMark at EBI, UK)
  • GRAIL (Exon recognition USA).
  • Gene feature (Exon recognition, Promoter and Transcription Factor Binding Site Prediction, Open Reading Frame Baylor College of Medicine (USA):
  • NetPlantGene (Prediction of splice sites in Arabidopsis at CBS, Denmark)
Find Transcriptional elements
  • SignalScan (Identification of transcriptional elements in <100 kb DNA sequences < 100 kb at BIMAS, University of Minesota, USA)
  • FirstEF (first-exon and promoter prediction program for human DNA at CSHL, USA)
Find t RNA
  • 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, France)
Other Tools
  • CountCodon (Analyse codon usage in protein coding sequence at Kazuasa DNA Research Institute, Jp)
  • DNA folding server (Fold secondary structures)
  • Netprimer (Free online primer analysis at Premier Biosoft Int., Ca, USA)
  • IMGT/V-QUEST an interactive tool for immunoglobulin and T cell receptor sequence analysis
  • MAR-Finder (Search for matrix association regions at NCGR, Santa Fe, USA)
  • Reverse Complement (Convert DNA sequence data to it's Reverse Complement.)
  • PRIDE (Primer design atDFKZ, Heidelberg, Germany)
  • 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)
DNA Sequence Analysis Tools