2011-12-23 05:43:34 +01:00
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The programs part of the Staden package provide a fully developed set
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of DNA sequence assembly, editing, analysis and more.
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Some of its features include:
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2012-02-19 21:20:37 +01:00
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GAP4 - Performs assembly, contig joining, assembly checking, repeat
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search, experiment suggestion, read pair analysis and contig
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editing.
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GAP5 - The new development version of Gap4, designed to work with the
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large volumes of data attainable through the newer sequencing
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technologies.
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PREGAP4 - Provides a graphical user interface to set up the processing
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required to prepare trace data for assembly or analysis.
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SPIN - Compares pairs of sequences in many ways, often presenting its
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results graphically and has a sliding sequence window linked to
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the plots.
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TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF
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trace files.
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2011-12-23 05:43:34 +01:00
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2012-02-19 21:20:37 +01:00
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For more information and citing, visit Staden's web page and check the
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2011-12-23 05:43:34 +01:00
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"References" file in the documentation.
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Notes:
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1) You should run the SlackBuild in real root environment (su -)!
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2012-02-19 21:20:37 +01:00
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2) Make sure you have Emacs and Tetex installed at build time.
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3) Although unsupported at the moment, SPIN can provide a GUI for the
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EMBOSS suite programs. If you want to give it a try, run as root
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"create_emboss_data" (EMBOSS should be installed, of course). This
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generates some files in /usr/share/staden/tcl/spin_emboss/acdtcl,
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so remember to manually clean them if you later uninstall staden.
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