Dna Sequence
TaxonDNA is a simple but extensible system for performing simple DNA (and other) sequence manipulations in Java. We hope to create a simple framework which can be quickly extended to create bioinformatics applications.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 380.94 KB | Download (58): TaxonDNA Download |
Permutations and combinations are often required in algorithms that do a complete search of the solution space. They are typically rather large so it's best not to compute them entirely but better to lazily generate them.This script uses Python generators to create appropriate generator objects,...
Platforms: Windows, Mac, *nix, Python, BSD Solaris
License: Freeware | Download (55): Generator for sequence operations Download |
Generators, introduced in Python 2.2, can be used to work with infinite sets. This script is a simple example of a generator that creates the Fibonacci sequence.Running this produces the following result:c:python22>python fib.py1 1 2 3 5 8 13 21 34
Platforms: Windows, Mac, *nix, Python, BSD Solaris
License: Freeware | Download (58): Fibonacci sequence using generators Download |
In one type of gene expression analysis, fluorescently tagged messenger RNA from different cells are hybridized to a microscopic array of thousands of complimentary DNA spots that correspond to different genes. Illuminated spots emit different color light, indicating which genes are expressed...
Platforms: Matlab
License: Freeware | Size: 4.35 MB | Download (46): DNA MicroArray Image Processing Case Study Download |
Maximum length sequence assuming distinctvalues = baseVal^powerVal-1 [ms]=mseqSearch(powerVal,baseVal) OUTPUT: ms: generated maximum length sequence, of length basisVal^powerVal-1 such that all values occur with equal frequency=basisVal except zero, which occurs basisVal-1 times INPUT: baseVal:...
Platforms: Matlab
License: Freeware | Size: 10 KB | Download (48): m-sequence generation program using a search algorithm 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 |
Sequence Generator (file ID #24620) has been renamed to CORE - Constraint Randomization Environment. Interface and code structure of v0.91 are explained in this manual.Current development concentrates on these topics:- Performance related issues- Bug fixes (3 known issues)- Improved constraint...
Platforms: Matlab
License: Freeware | Size: 614.4 KB | Download (44): Sequence Generator / CORE Manual (v0.91) Download |
Explore stretching just a single strand of DNA using optical tweezers or fluid flow. Experiment with the forces involved and measure the relationship between the stretched DNA length and the force required to keep it stretched. Is DNA more like a rope or like a spring?
Platforms: Mac
License: Freeware | Size: 1.47 MB | Download (35): Stretching DNA Download |
JMotifFinder is a small graphical utility I wrote to quickly find DNA Motifs such as Primers in huge EMBL Files. If you load an EMBL file containing exon and mRNA information into JMotifFinder, it will graphically display the location of the exons and mRNA within the source sequence. You can...
Platforms: Mac
License: Freeware | Size: 3.19 MB | Download (36): Motif Finder 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 |
BioFace is simple software for editing and analyzing DNA, RNA, and protein sequences that is written in Java using SWT and JFace as libraries. Opening GenBank, FASTA, EMBL, or simple sequence files and analizing these sequences can be done.
Platforms: *nix
License: Freeware | Size: 5.56 MB | Download (42): BioFace For Linux Download |
nebseq is a Python module for basic biological sequence manipulations. Import as usual >>> import nebseq Reverse complements The only note here is that revcomp does not check the input sequence to see if it looks like DNA or RNA. >>> nebseq.revcomp('ACGT') 'ACGT' >>>...
Platforms: *nix
License: Freeware | Size: 10.24 KB | Download (37): nebseq Download |
App::Session can represents a sequence of multiple events perhaps executed in separate processes. SYNOPSIS # ... official way to get a Session object ... use App; $session = App->context(); $context = $session->session(); # get the session # any of the following named parameters may be...
Platforms: *nix
License: Freeware | Size: 73.73 KB | Download (96): App::Session Download |
Bio::Tools::Run::PiseApplication::consensus is a Perl module. Bioperl class for: CONSENSUS Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo) References: G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein...
Platforms: *nix
License: Freeware | Size: 829.44 KB | Download (100): Bio::Tools::Run::PiseApplication::consensus Download |
The STed is the high-performance MIDI sequence editor / Music composer system. It had been working on X680x0 old Japanese personal workstation. The STed was originally developed by Mr. Takayuki "TURBO" Toda. Through many volunteers good office the source code of the STed has been opened. Since...
Platforms: *nix
License: Freeware | Size: 532.48 KB | Download (116): STed Download |
AlignAid is a Perl module that easily run sequence alignments locally or on a cluster. SYNOPSIS use AlignAid; # create an AlignAid object # a single, locally run blast job is the default my $job = AlignAid->new( db => my_blast_db, dir => $dir, fasta => my_query.fa, prog_args => V=20...
Platforms: *nix
License: Freeware | Size: 348.16 KB | Download (96): AlignAid Download |
Bio::Seq is a sequence object, with features. SYNOPSIS # This is the main sequence object in Bioperl # gets a sequence from a file $seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat); $seqobj = $seqio->next_seq(); # SeqIO can both read and write sequences; see Bio::SeqIO #...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (98): Bio::Seq Download |
Bio::PrimarySeqI is a Perl Interface definition for a Bio::PrimarySeq. SYNOPSIS # Bio::PrimarySeqI is the interface class for sequences. # If you are a newcomer to bioperl, you should # start with Bio::Seq documentation. This # documentation is mainly for developers using # Bioperl. #...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (92): Bio::PrimarySeqI Download |
Bio::Tools::CodonTable is a bioperl codon table object. SYNOPSIS # This is a read-only class for all known codon tables. The IDs are # the ones used by nucleotide sequence databases. All common IUPAC # ambiguity codes for DNA, RNA and animo acids are recognized. # to use use...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (127): Bio::Tools::CodonTable Download |
PM2V is a library for parallel encoding of a video sequence in MPEG II. PM2V is a project developed by students of the Ecole Nationale Supérieure dElectronique et de Radioelectronique de Bordeaux. ENSERB is a high national school of engineering based in Bordeaux (France). It has three...
Platforms: *nix
License: Freeware | Size: 184.32 KB | Download (100): pm2v build Download |