ETDs @PUC-Rio
| Título: | EXECUTION AND DATA AVAILABILITY CONTROL FOR APPLICATIONS ON BIOLOGICAL SEQUENCES: THE CASE OF BLAST | ||||||||||||||||||||||||||||||||||||
| Autor: |
MAIRA FERREIRA DE NORONHA |
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| Colaborador(es): |
SERGIO LIFSCHITZ - Orientador |
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| Catalogação: | 25/ABR/2007 | Língua(s): | PORTUGUESE - BRAZIL |
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| Tipo: | TEXT | Subtipo: | THESIS | ||||||||||||||||||||||||||||||||||
| Notas: |
[pt] Todos os dados constantes dos documentos são de inteira responsabilidade de seus autores. Os dados utilizados nas descrições dos documentos estão em conformidade com os sistemas da administração da PUC-Rio. [en] All data contained in the documents are the sole responsibility of the authors. The data used in the descriptions of the documents are in conformity with the systems of the administration of PUC-Rio. |
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| Referência(s): |
[pt] https://www.maxwell.vrac.puc-rio.br/projetosEspeciais/ETDs/consultas/conteudo.php?strSecao=resultado&nrSeq=9819&idi=1 [en] https://www.maxwell.vrac.puc-rio.br/projetosEspeciais/ETDs/consultas/conteudo.php?strSecao=resultado&nrSeq=9819&idi=2 |
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| DOI: | https://doi.org/10.17771/PUCRio.acad.9819 | ||||||||||||||||||||||||||||||||||||
| Resumo: | |||||||||||||||||||||||||||||||||||||
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This work consists on the creation of a tool named
BioProvider to provide
data to BLAST. The tool provides the data using buffer
management techniques
that are efficient for BLAST and controls process
scheduling. The communication
between BioProvider and the BLAST processes, as well as
the concurrency and
blocking control, is done through a device driver that
substitutes the read and
write function calls to the database files. By this means,
the application code can
remain unchanged and BioProvider can be used with
different versions of
BLAST. The development of BioProvider was the first stage
to the creation of a
solution that can be applied as well to other
Bioinformatics tools. Due to its
transparency in the view of other applications,
BioProvider can be easily extended
in the future to provide data to other applications, to
use other buffer management
techniques or to provide data stored in different formats
of those read by the client
processes, converting the data in runtime. BioProvider has
been tested with the
most recent version of NCBI BLAST and considerable
improvement has been
verified. The tool has been shown to work as well with the
open source version of
WU-BLAST. Some variations on the buffer management
algorithm were studied,
as well as the different factors that influence the
performance of BLAST
processes.
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