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Filtering by: Subject Nucleotide sequence -- Computer programs

Prediction of gene transcription start sites and initiation patterns from DNA sequence content

Creator:

Morton, Taj H.

Abstract:

The computational identification of gene Transcription Start Sites (TSSs) can provide insights into the regulation and function of genes without performing expensive experiments, particularly in organisms with incomplete annotations. High-resolution general-purpose TSS prediction remains a challenging problem, with little recent progress on the identification and differentiation of TSSs which are...

Resource Type:

Masters Thesis

Full Text:

(500 nt) from sequence content alone, but did not explore nucleotide- resolution models (Abeel et al
Algorithms for massive biological datasets

Creator:

Bryant, Douglas W. (Douglas Wesley)

Abstract:

Within the past several years the technology of high-throughput sequencing has transformed the study of biology by offering unprecedented access to life's fundamental building block, DNA. With this transformation's potential a host of brand-new challenges have emerged, many of which lend themselves to being solved through computational methods. From de...

Resource Type:

Dissertation

Full Text:

genome is over- sampled, resulting in many overlapping reads. A computer program designed for this
Improved parallel and sequential walking tree methods for biological string alignments

Creator:

Oregon State University. Dept. of Computer Science, Cull, Paul, 1943-, and Hsu, Tai C.

Abstract:

Approximate string matching is commonly used to align genetic sequences (DNA or RNA) to determine their shared characteristics. Most genetic string matching methods are based on the edit-distance model, which does not provide alignments for inversions and translocations. Recently, a heuristic called the Walking Tree Method [2, 3] has been...

Resource Type:

Research Paper

Full Text:

Computer Science Oregon State University Corvallis, OR 97331, USA 1. Abstract Approximate string