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Related Subjects
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This category includes brief overview of all related subjects.
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Defining BioInformatics
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In this section we tried to briefly explain what bioinformatics is ?
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Unviersities
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This contains information about universities that are offering bioinformatics degree programs.
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Resources
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Contains information about bioinformatics resources including databases, tools and techniques.
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Algorithms
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This category includes some of the basic algorithms that are usually used by bioinformaticians.
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Home » 2011 » August » 11 » DNA Sequence Analysis Tools
5:10 PM DNA Sequence Analysis Tools |
DNA sequence analysis tools
- 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)
- 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)
- 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)
- Find transcriptional elements
- 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)
- 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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