Staden Package
| Developer(s) | James Bonfield, Rodger Staden, et al. |
|---|---|
| Operating system | UNIX, Linux, Windows, Mac OS X |
| Type | Bioinformatics |
| License | open source |
| Website | http://staden.sourceforge.net/ |
The Staden Package is a set of open source tools for DNA sequence assembly, editing, and sequence analysis.
Package Components
The Staden package consists of a number of 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
- 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[1][2][3]. 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[4]. The Staden Package was converted to open source 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[5], the use of sequence quality scores to generate accurate consensus sequences[6], and the ZTR file format [7].
References
- ^ Staden R (1979). "A strategy of DNA sequencing employing computer programs". Nucleic Acids Res. 6: 2601--2610PMID461197.
- ^ Staden R (1984). "Computer methods to aid the determination and analysis of DNA sequences". Biochem Soc Trans. 12: 1005--1008PMID6397374.
- ^ Staden R, Beal KF, Bonfield JK (2000). "The Staden package, 1998". Methods Mol Biol. 132: 115--130PMID10547834.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ http://www.genomeweb.com/informatics/uk-s-mrc-ends-support-staden-package-first-sign-post-hgp-funding-priority-shift
- ^ Dear S, Staden R (1992). "A standard file format for data from DNA sequencing instruments". DNA Seq. 3: 107--110PMID1457811.
- ^ Bonfield JK, Staden R (1995). "The application of numerical estimates of base calling accuracy to DNA sequencing projects". Nucleic Acids Res. 23: 1406--1410PMID7753633.
- ^ Bonfield JK, Staden R (2002). "ZTR: a new format for DNA sequence trace data". Bioinformatics. 18: 3--10PMID11836205.