Staden Package

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Staden Package
Original author(s) Rodger Staden
Developer(s) James Bonfield, et al.
Initial release 1977; 40 years ago (1977)
Stable release
2.0.0b9 / 24 January 2012; 5 years ago (2012-01-24)
Preview release
2.0.0b11 / 25 April 2016; 13 months ago (2016-04-25)
Repository sourceforge.net/projects/staden
Development status Active
Written in C, C++, Fortran, Tcl
Operating system Unix, Linux, macOS, Windows
Platform IA-32, x86-64
Available in English
Type Bioinformatics
License BSD 3-clause
Website staden.sourceforge.net

The Staden Package is computer software, a set of tools for DNA sequence assembly, editing, and sequence analysis. It is open-source software, released under a BSD 3-clause license.

Package components[edit]

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[1]
  • Spin – DNA and protein sequence analysis

History[edit]

The Staden Package was developed by Rodger Staden's group at the Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, England, since 1977.[2][3][4] 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.[5] The package was converted to open source 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,[6] the use of sequence quality scores to generate accurate consensus sequences,[7] and the ZTR file format.[8]

See also[edit]

References[edit]

  1. ^ Bonfield JK, Whitwham A (2010). "Gap5—editing the billion fragment sequence assembly". Bioinformatics. 26 (14): 1699–1703. PMC 2894512Freely accessible. PMID 20513662. doi:10.1093/bioinformatics/btq268. 
  2. ^ Staden R (1979). "A strategy of DNA sequencing employing computer programs.". Nucleic Acids Res. 6 (7): 2601–2610. PMC 327874Freely accessible. PMID 461197. doi:10.1093/nar/6.7.2601. 
  3. ^ Staden R (1984). "Computer methods to aid the determination and analysis of DNA sequences.". Biochem Soc Trans. 12 (6): 1005–1008. PMID 6397374. doi:10.1042/bst0121005. 
  4. ^ Staden R, Beal KF, Bonfield JK (2000). "The Staden package, 1998.". Methods Mol Biol. 132: 115–130. PMID 10547834. doi:10.1385/1-59259-192-2:115. 
  5. ^ "UK s MRC Ends Support for Staden Package: First Sign of Post-HGP Funding Priority Shift?". Genomeweb. Genomeweb LLC. 5 May 2003. Retrieved 15 November 2016. 
  6. ^ Dear S, Staden R (1992). "A standard file format for data from DNA sequencing instruments.". DNA Seq. 3 (2): 107–110. PMID 1457811. doi:10.3109/10425179209034003. 
  7. ^ Bonfield JK, Staden R (1995). "The application of numerical estimates of base calling accuracy to DNA sequencing projects.". Nucleic Acids Res. 23: 1406–1410. PMC 306869Freely accessible. PMID 7753633. doi:10.1093/nar/23.8.1406. 
  8. ^ Bonfield JK, Staden R (2002). "ZTR: a new format for DNA sequence trace data.". Bioinformatics. 18: 3–10. PMID 11836205. doi:10.1093/bioinformatics/18.1.3. 

External links[edit]