Difference between revisions of "STADEN"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=Includes GAP4, GAP5, SPIN, TREV, and numerous smaller tools. | |sw summary=Includes GAP4, GAP5, SPIN, TREV, and numerous smaller tools. | ||
− | |bio method= | + | |bio method=Sequence assembly, Sequence alignment, Visualisation |
|bio tech=Sanger, 454, Illumina | |bio tech=Sanger, 454, Illumina | ||
+ | |interface=Desktop GUI, | ||
+ | |resource type=Desktop application | ||
|created by=R.Staden, S.Dear, J.Bonfield, K.Beal, et al. | |created by=R.Staden, S.Dear, J.Bonfield, K.Beal, et al. | ||
|created at=MRC Laboratory of Molecular Biology, Wellcome Trust Sanger Institute | |created at=MRC Laboratory of Molecular Biology, Wellcome Trust Sanger Institute | ||
Line 10: | Line 12: | ||
|sw feature=Integrated solution | |sw feature=Integrated solution | ||
|language=C, C++, Tcl, Fortran | |language=C, C++, Tcl, Fortran | ||
− | |licence=BSD, | + | |licence=BSD, |
|os=Linux, Windows, Mac OS X, UNIX, | |os=Linux, Windows, Mac OS X, UNIX, | ||
}} | }} |
Latest revision as of 14:07, 4 November 2016
Application data |
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Created by | R.Staden, S.Dear, J.Bonfield, K.Beal, et al. |
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Principal bioinformatics method(s) | Sequence assembly, Sequence alignment, Visualisation |
Technology | Sanger, 454, Illumina |
Created at | MRC Laboratory of Molecular Biology, Wellcome Trust Sanger Institute |
Maintained? | Yes |
Input format(s) | SAM, BAM, FASTA, Experiment Files, ZTR, AB1, SCF |
Output format(s) | SAM, FASTA, FASTQ |
Software features | Integrated solution |
Programming language(s) | C, C++, Tcl, Fortran |
Interface type(s) | Desktop GUI |
Resource type(s) | Desktop application |
Licence | BSD |
Operating system(s) | Linux, Windows, Mac OS X, UNIX |
Summary: Includes GAP4, GAP5, SPIN, TREV, and numerous smaller tools.
"Error: no local variable "counter" was set." is not a number.
A collection of tools for sequence processing, assembly, editing and analysis.
It is probably best known for Gap4 - a widely used tool for "finishing" sequencing projects. More recently Gap5 has been produced to handle the larger volumes of data that come from modern sequencing instruments. Both are supported for now, until Gap5 matures and acquires more features out of Gap4.
The Spin program performs DNA and protein sequence analysis, replacing the older sip, nip and pip programs from earlier Staden Package releases. Spin also provides a graphical interface to the EMBOSS package. Unfortunately spin is largely unsupported now (please contact us if you have free time).
Links
References
- . 2000. Methods Mol Biol
- . 2002. Bioinformatics
- . 2002. Bioinformatics
- . 1992. DNA Sequence
- . 1991. Nucleic Acids Research
- . 2010. Bioinformatics
- . 1984. Nucleic Acids Research
- . 1982. Nucleic Acids Research
- . 1995. Nucleic Acids Research
- . 1995. Nucleic Acids Research
- . 1996. DNA Sequence
- . 1998. Nucleic Acids Research
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