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News:

SeqCruncher™ improves DeCypher and CodeQuest throughput by 3-20X

TimeLogic welcomes new customers at NIEHS, Hiram College and the Korea National Institutes of Health

DeCypher 7.6.2 software update improves HMM analysis, output formatting

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Get Acrobat ReaderTechnical 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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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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