Repetitive Dna Sequences
MyCGR is an Objective-Caml library and a collection of tools to use the Chaos Game Representation on DNA sequences. MyCGR can empirically check the level and power of the tests and apply them on DNA sequences. It can generalize the dinucleotide abundance profile to a CGR-based relative...
Platforms: *nix
License: Freeware | Size: 1.8 MB | Download (97): MyCGR Download |
JDSA is a Java program that will degenerately search DNA sequences. This program searches sequences for multiple nucleotides at a given position (positional degeneracy), limited overall sequence accuracy (group degeneracy) or variable spacing between multiple DNA sequences (spacing degeneracy)....
Platforms: Mac
License: Freeware | Size: 51.2 KB | Download (40): JDSA Download |
ProteinMusic is a Java program converting DNA sequences into music. The original idea for this project came from R. D. King at the University of Wales, Aberystwyth and C. G Angus from the Shamen (King, R.D. & Angus, C.G. (1996)).
Platforms: Mac
License: Freeware | Size: 204.8 KB | Download (36): ProteinMusic Download |
Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 14.85 MB | Download (48): Bowtie Download |
Cleaver is a program for comparing restriction endonuclease digests of orthologous DNA sequences from different taxa. It performs virtual restriction digests and searches for endonucleases that cleave DNA fragments from given taxa but not others.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 4.49 MB | Download (52): Cleaver Download |
FSA is a probabilistic multiple sequence alignment algorithm which uses a 'distance-based' approach to aligning homologous protein, RNA or DNA sequences.
Platforms: Mac, BSD, Linux
License: Freeware | Size: 9.61 MB | Download (53): FSA Download |
A database to handle voucher specimens of DNA sequences used for molecular phylogenetics.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 1.23 MB | Download (53): NSG's voucher specimen database Download |
ProteinMusic is a Java program converting DNA sequences into music. The original idea for this project came from R. D. King at the University of Wales, Aberystwyth and C. G Angus from the Shamen (King, R.D. & Angus, C.G. (1996)).
Platforms: Windows, Mac, BSD, Linux
License: Freeware | Size: 206.88 KB | Download (48): ProteinMusic Download |
Find restriction enzymes that help differ known homologe DNA sequences (RFLP). Simulate electrophoresis gels. Usefull to investigate the diversity of a population by one of their common genes. Written in perl, uses bioperl modules and the GD library.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 10.84 KB | Download (51): RFLP planner Download |
The TandemSearcher is a Java based application for searching for tandem repeats in the DNA sequences. It is based on the Burrows-Wheeler Transform (BWT).
Platforms: Windows, Mac, Linux
License: Freeware | Size: 43.24 KB | Download (43): TandemSearcher Download |
The YeastsIdentification is a Java based application for searching for unique DNA sequences. It is based on the Burrows-Wheeler Transform (BWT).
Platforms: Windows, Mac, Linux
License: Freeware | Size: 139.23 KB | Download (43): YeastsIdentification Download |
ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies...
Platforms: *nix
License: Freeware | Size: 40.96 KB | Download (39): ESTScan Download |
JBoss DNA is a repository and set of tools that make it easy to capture, version, analyze, and understand the fundamental building blocks of information.As models, service and process definitions, schemas, source code, and other artifacts are added to the repository, JBoss DNA "sequences" the...
Platforms: Java
License: Freeware | Size: 4.71 MB | Download (44): JBoss DNA Download |
This package includes a modified version of dnapars.exe from Phylip 3.6. The orignal dnapars,exe uses a menu for settings of parameters. I changed it into a command-line driven one, called mbetoolbox_dnapars.exe. Then I built a MATLAB interface for it. Within MATLAB, after setting the path, set...
Platforms: Matlab
License: Freeware | Size: 307.2 KB | Download (40): PHYLIP DNA parsimony (dnapars) GUI Download |
Serial Cloner is a light molecular biology software. Serial Cloner reads and write DNA Strider-compatible files and import and export files in the universal FASTA format (as well as in pDRAW32 format). Powerful graphical display tools and simple interfaces help the analysis and construction steps...
Platforms: Mac
License: Freeware | Download (111): Serial Cloner Download |
Main Workbench includes all features from CLC DNA Workbench, CLC RNA Workbench, and CLC Protein Workbench, as well as a range of Gene Expression Analysis.
CLC Main Workbench creates a software environment enabling users to make a large number of advanced protein sequence analyses, combined with...
Platforms: Windows, XP, Windows Vista, XPX64, 7, 7x64
License: Freeware | Download (445): CLC Main Workbench Download |
NCBI has an implementation of BLAST algorithm on their website at www.ncbi.nlm.nih.gov/BLAST, which is good if you want to query short DNA or protein sequence against various sequence databases. The problem arises when large sequences need to be BLAST'ed against a sequence database or against...
Platforms: Matlab
License: Freeware | Size: 10 KB | Download (45): GUI for Basic Local Alignment Search Tool (BLAST) Download |
FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
Platforms: *nix
License: Freeware | Size: 9.61 MB | Download (39): FSA For Linux Download |
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human...
Platforms: *nix
License: Freeware | Size: 7.34 MB | Download (35): Bowtie for Linux Download |
Algorithm::NeedlemanWunsch is a sequence alignment with configurable scoring. SYNOPSIS use Algorithm::NeedlemanWunsch; sub score_sub { if (!@_) { return -2; # gap penalty } return ($_[0] eq $_[1]) ? 1 : -1; } my $matcher = Algorithm::NeedlemanWunsch->new(&score_sub); my $score =...
Platforms: *nix
License: Freeware | Size: 10.24 KB | Download (105): Algorithm::NeedlemanWunsch Download |