Staden Package

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.

Contents

Package Components

The Staden package consists of a number of different programs. The main components are:

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

  1. ^ Staden R (1979). "A strategy of DNA sequencing employing computer programs.". Nucleic Acids Res 6 (7): 2601–2610PMID461197. doi:10.1093/nar/6.7.2601. PMC 327874. PMID 461197. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=327874. 
  2. ^ Staden R (1984). "Computer methods to aid the determination and analysis of DNA sequences.". Biochem Soc Trans 12: 1005–1008PMID6397374. PMID 6397374. 
  3. ^ Staden R, Beal KF, Bonfield JK (2000). "The Staden package, 1998.". Methods Mol Biol 132: 115–130PMID10547834. PMID 10547834. 
  4. ^ http://www.genomeweb.com/informatics/uk-s-mrc-ends-support-staden-package-first-sign-post-hgp-funding-priority-shift
  5. ^ Dear S, Staden R (1992). "A standard file format for data from DNA sequencing instruments.". DNA Seq 3: 107–110PMID1457811. PMID 1457811. 
  6. ^ Bonfield JK, Staden R (1995). "The application of numerical estimates of base calling accuracy to DNA sequencing projects.". Nucleic Acids Res 23: 1406–1410. doi:10.1093/nar/23.8.1406. PMC 306869. PMID 7753633. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=306869. 
  7. ^ Bonfield JK, Staden R (2002). "ZTR: a new format for DNA sequence trace data.". Bioinformatics 18: 3–10PMID11836205. doi:10.1093/bioinformatics/18.1.3. 

External links

See also