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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)
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- 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)
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- 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)
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- 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)
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- 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)
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- 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)
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Find Transcriptional elements |
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- 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)
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- tRNAscan-SE (Search for tRNA genes in genomic sequence at Washington University, St Louis, US)
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- FAStRNA (Predict potential tRNA genes in genomic sequences at Institut Pasteur, Paris, France)
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- 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
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- 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)
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