CrocoBLAST: Running BLAST efficiently in the age of
next-generation sequencing

J 2017

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing

TRISTAO RAMOS, Ravi José, Allan Cézar DE AZEVEDO MARTINS, Gabrielle DA SILVA DELGADO, Crina-Maria IONESCU, Peter Turán ÜRMÉNYI et. al.

Basic information

Original name

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing

Authors

TRISTAO RAMOS, Ravi José (76 Brazil, belonging to the institution), Allan Cézar DE AZEVEDO MARTINS (76 Brazil), Gabrielle DA SILVA DELGADO (76 Brazil), Crina-Maria IONESCU (642 Romania, belonging to the institution), Peter Turán ÜRMÉNYI (76 Brazil), Rosane SILVA (76 Brazil) and Jaroslav KOČA (203 Czech Republic, guarantor, belonging to the institution)

Edition

Bioinformatics, Oxford, Oxford University Press, 2017, 1367-4803

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.481

RIV identification code

RIV/00216224:14310/17:00099996

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1093/bioinformatics/btx465

UT WoS

000415074800020

Keywords in English

sequence analysis; genomics; genome annotation; BLAST

Abstract

V originále

CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss. CrocoBLAST is freely available online, with ample documentation (webchem.ncbr.muni.cz/Platform/App/CrocoBLAST). No installation or user registration is required. CrocoBLAST is implemented in C, while the graphical user interface is implemented in Java. CrocoBLAST is supported under Linux and Windows, and can be run under Mac OS X in a Linux virtual machine.

Links

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

TRISTAO RAMOS, Ravi José, Allan Cézar DE AZEVEDO MARTINS, Gabrielle DA SILVA DELGADO, Crina-Maria IONESCU, Peter Turán ÜRMÉNYI, Rosane SILVA and Jaroslav KOČA. CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. Bioinformatics. Oxford: Oxford University Press, 2017, vol. 33, No 22, p. 3648-3651. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btx465.

@article{1408017,
   author = {Tristao Ramos, Ravi José and de Azevedo Martins, Allan Cézar and da Silva Delgado, Gabrielle and Ionescu, CrinaandMaria and Ürményi, Peter Turán and Silva, Rosane and Koča, Jaroslav and de Azevedo Martins, Allan Cézar and da Silva Delgado, Gabrielle},
   article_location = {Oxford},
   article_number = {22},
   doi = {http://dx.doi.org/10.1093/bioinformatics/btx465},
   keywords = {sequence analysis; genomics; genome annotation; BLAST},
   language = {eng},
   issn = {1367-4803},
   journal = {Bioinformatics},
   title = {CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing},
   url = {https://academic.oup.com/bioinformatics/article-abstract/33/22/3648/4004881},
   volume = {33},
   year = {2017}
}

TY  - JOUR
ID  - 1408017
AU  - Tristao Ramos, Ravi José - de Azevedo Martins, Allan Cézar - da Silva Delgado, Gabrielle - Ionescu, Crina-Maria - Ürményi, Peter Turán - Silva, Rosane - Koča, Jaroslav - de Azevedo Martins, Allan Cézar - da Silva Delgado, Gabrielle
PY  - 2017
TI  - CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing
JF  - Bioinformatics
VL  - 33
IS  - 22
SP  - 3648-3651
EP  - 3648-3651
PB  - Oxford University Press
SN  - 13674803
KW  - sequence analysis
KW  - genomics
KW  - genome annotation
KW  - BLAST
UR  - https://academic.oup.com/bioinformatics/article-abstract/33/22/3648/4004881
L2  - https://academic.oup.com/bioinformatics/article-abstract/33/22/3648/4004881
N2  - CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss. CrocoBLAST is freely available online, with ample documentation (webchem.ncbr.muni.cz/Platform/App/CrocoBLAST). No installation or user registration is required. CrocoBLAST is implemented in C, while the graphical user interface is implemented in Java. CrocoBLAST is supported under Linux and Windows, and can be run under Mac OS X in a Linux virtual machine.
ER  -

TRISTAO RAMOS, Ravi José, Allan Cézar DE AZEVEDO MARTINS, Gabrielle DA SILVA DELGADO, Crina-Maria IONESCU, Peter Turán ÜRMÉNYI, Rosane SILVA and Jaroslav KOČA. CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. \textit{Bioinformatics}. Oxford: Oxford University Press, 2017, vol.~33, No~22, p.~3648-3651. ISSN~1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btx465.

Detailed Information on Publication Record