Improved Alignment of Protein Sequences Based on Common Parts
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F08%3A00101243" target="_blank" >RIV/00216208:11320/08:00101243 - isvavai.cz</a>
Result on the web
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DOI - Digital Object Identifier
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Alternative languages
Result language
angličtina
Original language name
Improved Alignment of Protein Sequences Based on Common Parts
Original language description
In the last twenty years, protein databases have been growing exponentially. To speed up the search, heuristic approaches have been proposed and their accuracy has been steadily growing, but exact search is still needed in some cases. The only exact search algorithm remains SSEARCH (or it?s clones) which sequentially scans database of protein sequences, and performs full alignment against each of the sequences. Due to the need of the exact search, we focus on improving the sequential search algorithm. We decrease the costs needed to compute the alignment of pair of protein sequences when used with large databases. This is achieved by reusing alignment calculations of common parts of the sequences without loss of accuracy. With this method, we reduced the computational costs by up to 20 % depending on the database size and subset used. We also implemented approximate search which further reduced computational costs for the the sake of some accuracy loss.
Czech name
Vylepšené zarovnání proteinových sekvencích založené na společných částech
Czech description
Vylepšené zarovnání proteinových sekvencích založené na společných částech
Classification
Type
D - Article in proceedings
CEP classification
JC - Computer hardware and software
OECD FORD branch
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Result continuities
Project
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Continuities
Z - Vyzkumny zamer (s odkazem do CEZ)
Others
Publication year
2008
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Article name in the collection
ISBRA 2008: Bioinformatics Research and Applications
ISBN
978-3-540-79449-3
ISSN
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e-ISSN
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Number of pages
13
Pages from-to
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Publisher name
Springer
Place of publication
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Event location
Neuveden
Event date
Jan 1, 2008
Type of event by nationality
WRD - Celosvětová akce
UT code for WoS article
000255941000008