CAP3 EST assembly visualization and SNP discovery

Alexander Kozik akozik at atgc.org
Tue Mar 9 15:42:30 EST 2004


<x-flowed>Updated version of CAP3 EST assembly viewer is available at:
http://www.atgc.org/Py_ContigViewer/

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 (Arabidopsis, for example)
with intron position(s) to selected contig.
Screenshot of Contig Viewer in the extended mode is available at:
http://www.atgc.org/Py_ContigViewer/contig_viewer_blast_03.png

Contig Viewer works in conjunction with DIS
(Deletion, Insertion, Substitution) SNP discovery pipeline:
http://www.atgc.org/SNP_Discovery/

Contig Viewer and DIS pipeline have been tested on the
assembly of 43,737 tomato ESTs of three different 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.

Contig Viewer and DIS pipeline also have been tested on
Arabidopsis EST assembly represented by one genotype:
http://www.atgc.org/Py_ContigViewer/Arabidopsis/
Visualization of the assembly can reveal interesting examples:
with possible alternative spliced ESTs in the assembly
http://www.atgc.org/Py_ContigViewer/Arabidopsis/ATH_Contig5584_Alignment.png
with the set of paralogs assembled into one contig:
http://www.atgc.org/Py_ContigViewer/Arabidopsis/ATH_Contig660_Alignment.png
and other cases:
http://www.atgc.org/Py_ContigViewer/Arabidopsis/ATH_Contig5295_Alignment.png

I am particularly interested in the explanation of the last case.
I would like to know is it a real point mutation, or a systematic
sequencing error which may lead to false prediction of SNPs.

Feedback and comments are very welcome,

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


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