|
 Technical
Whitepapers
The following technical whitepapers
provide a detailed discussion of TimeLogic products and research
projects.
GeneDetective™ Poster,
presented at RECOMB2004
Abstract
The availability of large sequence databases and completed genomes
have made the mapping of cDNA or protein sequences onto genomic
sequences an important genomics analysis technique [4, 7, 2,
1]. Knowledge of the exact location of the exons is necessary
to design probes to be used for the detection of polymorphism
within a specific exon. At the same time, it is important to
know the locations of noncoding regions in order to study regulatory
processes. New genes and their exon structure can be predicted
by matching the sequences of homologous proteins from other species
onto a new genome [2, 1]. Another aspect of gene-modeling is
the search for alternative splice forms of a gene. Alternative
splicing is thought to be a way to expand the gene repertoire,
as the alternative splice forms of a gene may have different
or attenuated functions.
Here
we describe a software tool that finds the exons and introns
of a gene and constructs a gene model
with correct splice sites. This is achieved by aligning a cDNA
or amino acid sequence to a genomic DNA sequence using a double
affine Smith-Waterman algorithm with the second gap extension
penalty set to 0. This allows long gaps to span across the
introns. These intron-spanning gaps are expected to start and
end close
to (but not exactly) the appropriate splice donor and acceptor
sites. Therefore, the alignments are modified such that intron-spanning
gaps start and end at canonical splice sequence motifs.
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Poster
Gene-BLAST™: An Extension to the
BLAST Program
Abstract
We have introduced an improvement to the
BLAST algorithm, called Gene-BLAST™ that increases sensitivity
compared to other BLAST implementations. The improved sensitivity
is the result of the use of dynamic programming in the alignment
phase that allows for the crossing of introns. In addition to providing
a better look at the match between query and target, some small
regions may be found that would show up amongst the rest of the
hits.Gene-BLAST works with both protein and nucleotide data, and
is accelerated on the DeCypher system, providing high throughput
in addition to high sensitivity.
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