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=Assembly, Alignment, | + | |bio method=Assembly, Alignment, Visualization |
|bio tech=Sanger, 454, Illumina | |bio tech=Sanger, 454, Illumina | ||
|created by=R.Staden, S.Dear, J.Bonfield, K.Beal, et al. | |created by=R.Staden, S.Dear, J.Bonfield, K.Beal, et al. |
Revision as of 20:53, 10 September 2010
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) | Assembly, Alignment, Visualization |
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 |
Licence | BSD |
Operating system(s) | Linux, Unix, Windows, (partially) MacOS X |
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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