CAP3 Contig Viewer and SNP discovery

Alexander Kozik akozik at atgc.org
Tue Mar 9 08:17:48 EST 2004

Updated version of CAP3 EST assembly viewer is available at:

Python Contig Viewer, a stand alone cross-platform desktop
application uses CAP3 alignments to graphically display
and validate candidate SNPs and InDels. Contig Viewer
also simplifies PCR oligo design in an interactive mode.

The extended mode of Contig Viewer provides the display
of BLAST hits of annotated sequences with intron position(s)
to selected contig. Screenshot of Contig Viewer in the
extended mode is available at:

Contig Viewer works in conjunction with DIS
(Deletion, Insertion, Substitution) SNP discovery pipeline:

Contig Viewer and DIS pipeline have been tested on the
assembly of 43,737 tomato ESTs of three genotypes
(Lycopersicon esculentum, L. hirsutum and L. pennellii).
Our method revealed more than 1000 SNP/InDel candidates of
high level of confidence on the example tomato assembly
represented by ~3,800 contigs.

Feedback and comments are very welcome,

Alexander Kozik,
Department of Vegetable Crops,
UC Davis, CA


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