Staden Package
Encyclopedia
The Staden Package is a set of open source tools for DNA sequence assembly
, editing, and sequence analysis.
in 2004, and new versions were released in 2004, 2005, and 2009.
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.
Sequence assembly
In bioinformatics, sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology cannot read whole genomes in one go, but rather reads small pieces of between 20 and 1000 bases,...
, editing, and sequence analysis.
Package Components
The Staden package consists of a number of different programs. The main components are:- pregap4 - base calling with PhredPhredPhred may refer to:*Phred base calling, a program used in molecular biology*Phred quality score, a term used in molecular biology*Phred , a character from the comic strip Doonesbury*The Phred on Your Head Show, a children's television show...
, end clipping, and vector trimming. - trev - trace viewing and editing
- gap4 - sequence assembly, contig editing, and finishing
- Spin - DNA and protein sequence analysis
History
The Staden Package was developed by Rodger Staden's group at the MRC Cambridge in England since 1977. The Staden package was available free to academic users, with 2500 licenses issued in 2003 and an estimated 10,000 users, when funding for further development was cut. The Staden Package was converted to open sourceOpen source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
in 2004, and new versions were released in 2004, 2005, and 2009.
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.
External links
See also
- PhredPhred base callingPhred base-calling is a computer program for identifying a base sequence from a fluorescence "trace" data generated by an automated DNA sequencer that uses electrophoresis and 4-fluorescent dye method. When originally developed, Phred produced significantly fewer errors in the data sets examined...
- PhrapPhrapPhrap 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 Human Genome Project...
- ConsedConsedConsed 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 :...
- CodonCode AlignerCodonCode AlignerCodonCode Aligner is a commercial application for DNA sequence assembly, sequence alignment, and editing on Mac OS X and Windows.- Features :* Chromatogram editing, end clipping, and vector trimming.* Sequence assembly and contig editing...
- GeneiousGeneiousGeneious is suite of cross-platform bioinformatics software applications developed by Biomatters Ltd.- Features :Geneious comes in a Basic version that is free for academic use, and a commercial Pro version with added features. Geneious bundles various bioinformatics tools under one hood with an...
- MacVectorMacVectorMacVector 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.- Features :...
- UGENEUGENEUGENE is free open-source cross-platform bioinformatics software.It integrates dozens of well-known biological tools and algorithms, providing both graphical user and command line interfaces...
- Vector NTIVector NTIVector NTI is a bioinformatics software package. The current versions are v11.5.1 for Windows/PCs and v7.1 for Macs, but only supporting Mac OS X v10.3 .- Features :* create, annotate, analyse, and share DNA/protein sequences...