DNA Sequence Analysis Tools

Restriction, Detect repeats & unusual Patterns

  • Restrictionmapper

  • 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>

  • Zinfo (Detection of unusual sequences in large DNAs at Virtual Genome Center), USA)

  • REPuter (Fast computation of maximal repeats in complete genomes at Bielefeld University, Germany)

  • LALIGN (Finds multiple matching subsegments in two sequences at EMBnet, Swiss node)

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 Identification.at Baylor College of Medicine (USA):

  • NetPlantGene (Prediction of splice sites in Arabidopsis at CBS, Denmark)

Find Transcriptional elements

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)

  • CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer design at the Weizmann Institute, Israel)