Dna Sequence Assembly

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

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

Asm2class is a java assembly to class file compiler. Asm2class is release under the terms of the GPL License. The current version of asm2class (0.1.2) is a beta version and allow generating class file from java assembly file that contains class definition, field definition, method definition... Platforms: *nix

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

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

revava is a single pass disassembler that reads in a file containing a program intended for an Atmel AVR microcontroller and outputs assembly code that can be input to an avr assembler. The output of revava contains assembler mnemonics where possible and dc.W declarations where no mnemonic... Platforms: *nix

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

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

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

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

PikLoops is a simple KDE program used to generate assembly time delays for Microchip microcontrolers using Microchip instructions. PikLoops is based on a program for Windows, originally created by William J. Boucher. Using his calculation formulas we can generate accurate assembly language time... Platforms: *nix

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

Boxtream is both an audio and video encoder and streamer and an assembly of audio and video hardware, forming a mobile video streaming studio. It is designed to easily record and stream live presentations including a presenter and synchronized slides, or slides only, or presenter only, and was... Platforms: *nix

GNU lightning is a library that generates assembly language code at run-time; it is very fast, making it ideal for Just-In-Time compilers, and it abstracts over the target CPU, as it exposes to the clients a standardized RISC instruction set inspired by the MIPS and SPARC chips. GNU lightning... Platforms: *nix

Mono-Readline is a simple little assembly for .Net (specifically Mono) that provides support for GNU Readline support within Mono applications. Mono-Readline project is based on the code of Martin Baulig in the Mono debugger. I just took it and made it all nice and autoconf/automake enabled.... Platforms: *nix

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

Bio::AlignIO::bl2seq is a bl2seq sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class, as in: use Bio::AlignIO; $in = Bio::AlignIO->new(-file => "inputfilename" , -format => bl2seq); $aln = $in->next_aln(); This object can create... Platforms: *nix

Bio::AlignIO::msf is a Perl module with msf sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. This object can transform Bio::Align::AlignI objects to and from msf flat file databases. The rest of the documentation details each of... Platforms: *nix

NeoBio project consists of Bioinformatics algorithms in Java. What algorithms? The current version consists mainly of (pairwise) sequence alignment algorithms such as the classical dynamic programming methods of Needleman & Wunsch (global alignment) and Smith & Waterman (local alignment).... Platforms: *nix

CTAL_0 is an extension of Typed Assembly Language, and an experimental C compiler that generates CTAL0 assembly code. Usage: 1. First, download the source code and extract it. 2. Next, make in ctalz-software directory. 3. The compiler can be invoked by shell script ctc. If compilation... Platforms: *nix