staden - 2.0.0+b11-4 main

Staden is a fully developed set of DNA sequence assembly (Gap4 and
Gap5), editing and analysis tools (Spin).
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Gap4 performs sequence assembly, contig ordering based on read pair
data, contig joining based on sequence comparisons, assembly checking,
repeat searching, experiment suggestion, read pair analysis and contig
editing. It has graphical views of contigs, templates, readings and
traces which all scroll in register. Contig editor searches and
experiment suggestion routines use confidence values to calculate the
confidence of the consensus sequence and hence identify only places
requiring visual trace inspection or extra data. The result is
extremely rapid finishing and a consensus of known accuracy.
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Pregap4 provides a graphical user interface to set up the processing
required to prepare trace data for assembly or analysis, and automates
these processes.
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Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and
ZTR trace files.
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Prefinish analyses partially completed sequence assemblies and suggests
the most efficient set of experiments to help finish the project.
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Tracediff and hetscan automatically locate mutations by comparing trace
data against reference traces. They annotate the mutations found ready
for viewing in gap4.
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Spin analyses nucleotide sequences to find genes, restriction sites,
motifs, etc. It can perform translations, find open reading frames,
count codons, etc. Many results are presented graphically and a sliding
sequence window is linked to the graphics cursor. Spin also compares
pairs of sequences in many ways. It has very rapid dot matrix analysis,
global and local alignment algorithms, plus a sliding sequence window
linked to the graphical plots. It can compare nucleic acid against
nucleic acid, protein against protein, and protein against nucleic
acid.