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The alignment manager.

Wheelan, Sarah Jo.

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The alignment manager.

Record Type:	Electronic resources : Monograph/item
Title/Author:	The alignment manager./
Author:	Wheelan, Sarah Jo.
Description:	246 p.
Notes:	Source: Dissertation Abstracts International, Volume: 64-02, Section: B, page: 0531.
Contained By:	Dissertation Abstracts International64-02B.
Subject:	Biology, Genetics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3080794

The alignment manager.
Wheelan, Sarah Jo.

The alignment manager. - 246 p.

Source: Dissertation Abstracts International, Volume: 64-02, Section: B, page: 0531.

Thesis (Ph.D.)--The Johns Hopkins University, 2003.

Sequence alignments are difficult entities to manipulate computationally with currently available tools. The new alignment manager, a function layer between application programs and NCBI seq-aligns, expands the methods available for accessing alignments and alignment sets, and resolves a weakness in the NCBI data model. The NCBI data model includes seq-aligns, numerical representations of alignments. The NCBI toolkit provides methods to transform just about any input alignment into a seq-align, which efficiently represents starts and stops for storage on disk; however, seq-aligns are not optimally efficient for computations. The alignment manager provides a simple interface to single alignments, and can combine sets of alignments into pseudo-multiple alignments for access. The alignment manager can handle just about any type of alignment, including discontinuous, and is capable of representing complex relationships among sequences. Once the alignment manager was written it became possible to write many applications using it to manipulate sequence alignments. The program, Spidey, is one such example. Spidey aligns spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment. Spidey can quickly produce reliable alignments even when confronted with noise from alternative splicing, polymorphisms, sequencing errors or evolutionary divergence. Spidey was used to align reference sequences to known genomic sequences and then to the draft human genome, to align mRNAs to gene clusters, and to align mouse mRNAs to human genomic sequence. We compared Spidey to two other spliced alignment programs, and Spidey generally performed quite well in a very reasonable amount of time. In general, using the alignment manager improves the speed of an application while increasing its capabilities.Subjects--Topical Terms:

1017730
Biology, Genetics.

The alignment manager.
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500 $a Source: Dissertation Abstracts International, Volume: 64-02, Section: B, page: 0531.
500 $a Advisers: James Ostell; Thomas Kelly.
502 $a Thesis (Ph.D.)--The Johns Hopkins University, 2003.
520 $a Sequence alignments are difficult entities to manipulate computationally with currently available tools. The new alignment manager, a function layer between application programs and NCBI seq-aligns, expands the methods available for accessing alignments and alignment sets, and resolves a weakness in the NCBI data model. The NCBI data model includes seq-aligns, numerical representations of alignments. The NCBI toolkit provides methods to transform just about any input alignment into a seq-align, which efficiently represents starts and stops for storage on disk; however, seq-aligns are not optimally efficient for computations. The alignment manager provides a simple interface to single alignments, and can combine sets of alignments into pseudo-multiple alignments for access. The alignment manager can handle just about any type of alignment, including discontinuous, and is capable of representing complex relationships among sequences. Once the alignment manager was written it became possible to write many applications using it to manipulate sequence alignments. The program, Spidey, is one such example. Spidey aligns spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment. Spidey can quickly produce reliable alignments even when confronted with noise from alternative splicing, polymorphisms, sequencing errors or evolutionary divergence. Spidey was used to align reference sequences to known genomic sequences and then to the draft human genome, to align mRNAs to gene clusters, and to align mouse mRNAs to human genomic sequence. We compared Spidey to two other spliced alignment programs, and Spidey generally performed quite well in a very reasonable amount of time. In general, using the alignment manager improves the speed of an application while increasing its capabilities.
590 $a School code: 0098.
650 4 $a Biology, Genetics. $3 1017730
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773 0 $t Dissertation Abstracts International $g 64-02B.
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790 1 0 $a Kelly, Thomas, $e advisor
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