The Staden Package is computer
software
Software is a set of computer programs and associated software documentation, documentation and data (computing), data. This is in contrast to Computer hardware, hardware, from which the system is built and which actually performs the work.
...
, a set of tools for DNA
sequence assembly
In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one ...
, editing, and sequence analysis. It is
open-source software
Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Ope ...
, released under a
BSD
The Berkeley Software Distribution or Berkeley Standard Distribution (BSD) is a discontinued operating system based on Research Unix, developed and distributed by the Computer Systems Research Group (CSRG) at the University of California, Be ...
3-clause license.
Package components
The Staden package consists of several different programs. The main components are:
* pregap4 – base calling with
Phred, end clipping, and vector trimming
* trev – trace viewing and editing
* gap4 – sequence assembly, contig editing, and finishing
* gap5 – assembly visualising, editing, and finishing of NGS data
* Spin – DNA and protein sequence analysis
History
The Staden Package was developed by Rodger Staden's group at the
Medical Research Council (MRC)
Laboratory of Molecular Biology
The Medical Research Council (MRC) Laboratory of Molecular Biology (LMB) is a research institute in Cambridge, England, involved in the revolution in molecular biology which occurred in the 1950–60s. Since then it has remained a major medical r ...
, Cambridge, England, since 1977.
The package was available free to academic users, with 2,500 licenses issued in 2003 and an estimated 10,000 users, when funding for further development ended.
The package was converted to
open-source
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...
in 2004, and several new versions have been released since.
During the years of active development, the Staden group published a number of widely used file formats and ideas, including the SCF file format,
the use of sequence quality scores to generate accurate consensus sequences,
and the ZTR file format.
See also
*
Genome Compiler
Twist Bioscience is a public biotechnology company based in South San Francisco that manufactures synthetic DNA and DNA products for customers in a wide range of industries. Twist was founded in 2013 by Emily Leproust, Bill Banyai, and Bill P ...
*
Phred base calling Phred is a computer program for base calling, that is to say, identifying a nucleobase sequence from fluorescence "trace" data generated by an automated DNA sequencer that uses electrophoresis and 4-fluorescent dye method. When originally developed, ...
*
Phrap Phrap is a widely used program for DNA sequence assembly. It is part of the Phred-Phrap-Consed package.
History
Phrap was originally developed by Prof. Phil Green for the assembly of cosmids in large-scale cosmid shotgun sequencing within the ...
*
Consed
Consed is a program for viewing, editing, and finishing DNA sequence assemblies. Originally developed for sequence assemblies created with phrap, recent versions also support other sequence assembly programs like Newbler.
History
Consed was ...
*
CodonCode Aligner
CodonCode Aligner is a commercial application for DNA sequence assembly, sequence alignment, and editing on Mac OS X and Windows.
Features
Features include chromatogram editing, end clipping, and vector trimming, sequence assembly and contig e ...
*
MacVector
MacVector is a commercial sequence analysis application for Apple Macintosh computers running Mac OS X. It is intended to be used by molecular biologists to help analyze, design, research and document their experiments in the laboratory. MacVect ...
*
UGENE
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.
UGENE helps biolo ...
*
Vector NTI
References
External links
*{{Official website, staden.sourceforge.net
Bioinformatics software
Computational science