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 (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)

• 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)

• Identification of Prokaryotic Promoters (Promotor prediction in <100>

• IHF Site/Sigma 54 Promoter searches (at Pensylvania State University, USA

• SignalScan (Identification of transcriptional elements in <100>

• FirstEF (first-exon and promoter prediction program for human DNA at CSHL, USA)

• 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)

• 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)