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The Staden Package |
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Introduction
The Staden package of sequence programs contains a suite of programs for reading and
assembling sequencing gels. These programs are run through
X-windows and the command line. It also includes two
X-based programs which allow a variety of sequence analysis tasks, such as sequence
comparisons and gene finding, to be performed. The assembly programs can also be
made to use the Phred base caller and the Phrap, FakII or Cap3 Assembly programs.
The main X-based (see the X-guide) programs are:
- pregap4 - prepares sequence trace
data for analysis or assembly.
- trev - allows viewing and editing of
ABI, ALF or SCF trace files.
- gap4 - performs assembly, contig
joining, assembly checking, repeat searching, experiment suggestion, read pair
analysis and contig editing.
- sip4 - compares pairs of sequences. It
includes dot plots, finding matching words, global and local optimal alignments
and statistical evaluation of matches. Nucleotide sequences can be complemented
and translated to allow amino acid comparisons.
- nip4 - Analyses nucleotide sequences to find
genes, restriction sites and motifs. It will perform translations, find ORFs and
examine codon usage.
The command line programs are mainly called through pregap4 though they can be used
independently.
Documentation
Extensive documentation of the Staden package is available by the web as:
- A brief table of contents.
- A full table of contents.
- An index to the items in the manual.
- To get information on the main programs, see the links in the
introduction.
Last Modified 29/12/99 by
BRUHK support; Copyright ©* 1999 The University of Hong Kong
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