A parallel hash-based method for local sequence alignment

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14610%2F22%3A00136722" target="_blank" >RIV/00216224:14610/22:00136722 - isvavai.cz</a>

Výsledek na webu

<a href="https://onlinelibrary.wiley.com/doi/10.1002/cpe.6568" target="_blank" >https://onlinelibrary.wiley.com/doi/10.1002/cpe.6568</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/cpe.6568" target="_blank" >10.1002/cpe.6568</a>

Jazyk výsledku

angličtina

Název v původním jazyce

A parallel hash-based method for local sequence alignment

Popis výsledku v původním jazyce

Algorithms utilize an index-based aligning strategy, like a hash table, which typically entails the seed-and-extend method and is a time-consuming task. Here, we developed a hash-based search algorithm based on the SSAHA method without the use of seed-and-extend to conduct search and alignment faster than previous methods with multiple processors. In the proposed method by using the overlapping method in query and reference sequences, the accuracy and sensitivity increased. Further, the speed also increased by creating a hash table for the reference sequence when it was placed in the memory. Furthermore, by evaluating three datasets of different sequences in size and volumes, the effect of the created piece lengths as well as the effect of multiple processors on each dataset was evaluated indicating not only appeasing the time issue in alignment but also improving the mapping speed compared to the BLAST and SSAHA algorithms.

Název v anglickém jazyce

A parallel hash-based method for local sequence alignment

Popis výsledku anglicky

Algorithms utilize an index-based aligning strategy, like a hash table, which typically entails the seed-and-extend method and is a time-consuming task. Here, we developed a hash-based search algorithm based on the SSAHA method without the use of seed-and-extend to conduct search and alignment faster than previous methods with multiple processors. In the proposed method by using the overlapping method in query and reference sequences, the accuracy and sensitivity increased. Further, the speed also increased by creating a hash table for the reference sequence when it was placed in the memory. Furthermore, by evaluating three datasets of different sequences in size and volumes, the effect of the created piece lengths as well as the effect of multiple processors on each dataset was evaluated indicating not only appeasing the time issue in alignment but also improving the mapping speed compared to the BLAST and SSAHA algorithms.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10200 - Computer and information sciences

Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2022

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

CONCURRENCY AND COMPUTATION-PRACTICE &amp; EXPERIENCE

ISSN

1532-0626

e-ISSN

—

Svazek periodika

34

Číslo periodika v rámci svazku

3

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

16

Strana od-do

1-16

Kód UT WoS článku

000687967500001

EID výsledku v databázi Scopus

2-s2.0-85113346967