| 词条 | Staden Package |
| 释义 |
| name = Staden Package | logo = | screenshot = | caption = | author = Rodger Staden | developer = James Bonfield, et al. | released = {{Start date and age|1977}} | latest release version = 2.0.0b9 | latest release date = {{Start date and age|2012|01|24|df=yes}} | latest preview version = 2.0.0b11 | latest preview date = {{Start date and age|2016|04|25|df=yes}} | programming language = C, C++, Fortran, Tcl | operating system = Unix, Linux, macOS, Windows | platform = IA-32, x86-64 | size = | language = English | genre = Bioinformatics | license = BSD 3-clause | website = {{URL|staden.sourceforge.net}} | repo = {{URL|sourceforge.net/projects/staden}} | standard = | AsOf = }} 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 componentsThe Staden package consists of several different programs. The main components are:
HistoryThe 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{{Portal|Free and open-source software}}
References1. ^{{cite journal |doi=10.1093/bioinformatics/btq268|vauthors=Bonfield JK, Whitwham A |year=2010|title=Gap5—editing the billion fragment sequence assembly|journal=Bioinformatics|volume=26|pages=1699–1703|pmid=20513662|issue=14|pmc=2894512}} 2. ^{{cite journal |doi=10.1093/nar/6.7.2601 |author=Staden R|year=1979|title=A strategy of DNA sequencing employing computer programs. |pmc=327874|journal=Nucleic Acids Res|volume=6 |issue=7|pages=2601–2610|pmid=461197}} 3. ^{{cite journal |author=Staden R|year=1984|title=Computer methods to aid the determination and analysis of DNA sequences.|journal=Biochem Soc Trans|volume=12|pages=1005–1008|pmid=6397374|issue=6|doi=10.1042/bst0121005}} 4. ^{{cite journal |vauthors=Staden R, Beal KF, Bonfield JK |year=2000|title=The Staden package, 1998.|journal=Methods Mol Biol|volume=132|pages=115–130|pmid=10547834|doi=10.1385/1-59259-192-2:115}} 5. ^{{cite web |url=http://www.genomeweb.com/informatics/uk-s-mrc-ends-support-staden-package-first-sign-post-hgp-funding-priority-shift |title=UK s MRC Ends Support for Staden Package: First Sign of Post-HGP Funding Priority Shift? |author= |date=5 May 2003 |website=Genomeweb |publisher=Genomeweb LLC |access-date=15 November 2016}} 6. ^{{cite journal |vauthors=Dear S, Staden R |year=1992|title=A standard file format for data from DNA sequencing instruments.|journal=DNA Seq|volume=3|pages=107–110|pmid=1457811|doi=10.3109/10425179209034003|issue=2}} 7. ^{{cite journal |doi=10.1093/nar/23.8.1406 |vauthors=Bonfield JK, Staden R |year=1995|title=The application of numerical estimates of base calling accuracy to DNA sequencing projects.|journal=Nucleic Acids Res|volume=23|pages=1406–1410 |pmid=7753633 |pmc=306869}} 8. ^{{cite journal |doi=10.1093/bioinformatics/18.1.3 |vauthors=Bonfield JK, Staden R |year=2002|title=ZTR: a new format for DNA sequence trace data.|journal=Bioinformatics|volume=18|pages=3–10|pmid=11836205}} External links
2 : Bioinformatics software|Computational science |
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