Other Software

Help Pages for Facilities and Programs available at CHMCC and the UC Medical Center

MicroArray Basics A brief introduction

An Introduction to Genetic Sequence Analysis A short-course covering most facets of basic computerized sequence analysis.

GCG Sequence Analysis Programs Help Files from GCG. Available only from the UC and CHMCC campuses.

Celera Discovery System Help Pages (1.9 MB, requires Adobe Acrobat)

Phylip Phylogenetic Analysis Programs (from Joe Felsenstein, U Wash)

Swat
SWAT is a program for searching one or more DNA or protein query
sequences, or a query profile, against a sequence database, using (an
efficient implementation of) the Smith-Waterman or Needleman-Wunsch
algorithms, with linear (affine) gap penalties. For each match an
empirical measure of statistical significance derived from the observed
score distribution is computed.

Swat and Crossmatch
Swat and cross_match are programs for rapid protein and nucleic acid
sequence comparison and database search, based on an efficient
implementation of the Smith-Waterman-Gotoh algorithm (Smith &
Waterman 1981, Gotoh 1982).

Fragement Assembly Programs

Cap3 Fragment Assembly A short how-to document

Phred Phred reads DNA sequencer trace data, calls bases,
assigns quality values to the bases, and writes the base calls and
quality values to output files.

Phrap phrap ("phragment assembly program", or "phil's revised
assembly program"; a homonym of "frappe" = French for "swat") -- a
program for assembling shotgun DNA sequence data. Key features: allows
use of entire read (not just trimmed high quality part); uses a
combination of user-supplied and internally computed data quality
information to improve accuracy of assembly in the presence of repeats;
constructs contig sequence as a mosaic of the highest quality parts of
reads (rather than a consensus); provides extensive information about
assembly (including quality values for contig sequence) to assist
trouble-shooting; able to handle very large datasets.

Consed Consed is a program for viewing and editing assemblies assembled with the phrap assembly program.

PolyPhred PolyPhred is a program that helps to accurately
identify heterozygous sites in sequences produced with
fluorescence-based chemistries.