publication . Article . Other literature type . 2009

BLAST+: architecture and applications.

Christiam Camacho;
Open Access English
  • Published: 01 Dec 2009 Journal: BMC Bioinformatics (issn: 1471-2105, Copyright policy)
  • Publisher: BMC
Abstract
<p>Abstract</p> <p>Background</p> <p>Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications.</p> <p>Results</p> <p>We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long da...
Subjects
free text keywords: Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5, Biochemistry, Molecular Biology, Computer Science Applications, Software
26 references, page 1 of 2

Altschul, S, Gish, W, Miller, W, Myers, E, Lipman, D. Basic local alignment search tool. J Mol Biol. 1990; 215 (3): 403-410 [OpenAIRE] [PubMed]

Altschul, S, Madden, T, Schäffer, A, Zhang, J, Zhang, Z, Miller, W, Lipman, D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25 (17): 3389-3402 [OpenAIRE] [PubMed] [DOI]

NCBI C toolkit.

Zhang, Z, Schäffer, A, Miller, W, Madden, T, Lipman, D, Koonin, E, Altschul, S. Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res. 1998; 26 (17): 3986-3990 [OpenAIRE] [PubMed] [DOI]

Schäffer, A, Wolf, Y, Ponting, C, Koonin, E, Aravind, L, Altschul, S. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics. 1999; 15 (12): 1000-1011 [OpenAIRE] [PubMed] [DOI]

Schäffer, A, Aravind, L, Madden, T, Shavirin, S, Spouge, J, Wolf, Y, Koonin, E, Altschul, S. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 2001; 29 (14): 2994-3005 [OpenAIRE] [PubMed] [DOI]

Zhang, Z, Schwartz, S, Wagner, L, Miller, W. A greedy algorithm for aligning DNA sequences. J Comput Biol. ; 7 (1-2): 203-214 [OpenAIRE] [PubMed] [DOI]

A/G BLAST.

Waterston, R, Lindblad-Toh, K, Birney, E, Rogers, J, Abril, J, Agarwal, P, Agarwala, R, Ainscough, R, Alexandersson, M, An, P. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002; 420 (6915): 520-562 [OpenAIRE] [PubMed] [DOI]

RepeatMasker Web site.

NCBI BLAST web site.

Johnson, M, Zaretskaya, I, Raytselis, Y, Merezhuk, Y, McGinnis, S, Madden, T. NCBI BLAST: a better web interface. Nucleic Acids Res. 2008; 36 (Web Server issue): W5-9 [OpenAIRE] [PubMed] [DOI]

Kent, W. BLAT--the BLAST-like alignment tool. Genome Res. 2002; 12 (4): 656-664 [OpenAIRE] [PubMed]

Cameron, M, Williams, H, Cannane, A. A deterministic finite automaton for faster protein hit detection in BLAST. J Comput Biol. 2006; 13 (4): 965-978 [OpenAIRE] [PubMed] [DOI]

NCBI C++ toolkit documentation.

26 references, page 1 of 2
Abstract
<p>Abstract</p> <p>Background</p> <p>Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications.</p> <p>Results</p> <p>We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long da...
Subjects
free text keywords: Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5, Biochemistry, Molecular Biology, Computer Science Applications, Software
26 references, page 1 of 2

Altschul, S, Gish, W, Miller, W, Myers, E, Lipman, D. Basic local alignment search tool. J Mol Biol. 1990; 215 (3): 403-410 [OpenAIRE] [PubMed]

Altschul, S, Madden, T, Schäffer, A, Zhang, J, Zhang, Z, Miller, W, Lipman, D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25 (17): 3389-3402 [OpenAIRE] [PubMed] [DOI]

NCBI C toolkit.

Zhang, Z, Schäffer, A, Miller, W, Madden, T, Lipman, D, Koonin, E, Altschul, S. Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res. 1998; 26 (17): 3986-3990 [OpenAIRE] [PubMed] [DOI]

Schäffer, A, Wolf, Y, Ponting, C, Koonin, E, Aravind, L, Altschul, S. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics. 1999; 15 (12): 1000-1011 [OpenAIRE] [PubMed] [DOI]

Schäffer, A, Aravind, L, Madden, T, Shavirin, S, Spouge, J, Wolf, Y, Koonin, E, Altschul, S. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 2001; 29 (14): 2994-3005 [OpenAIRE] [PubMed] [DOI]

Zhang, Z, Schwartz, S, Wagner, L, Miller, W. A greedy algorithm for aligning DNA sequences. J Comput Biol. ; 7 (1-2): 203-214 [OpenAIRE] [PubMed] [DOI]

A/G BLAST.

Waterston, R, Lindblad-Toh, K, Birney, E, Rogers, J, Abril, J, Agarwal, P, Agarwala, R, Ainscough, R, Alexandersson, M, An, P. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002; 420 (6915): 520-562 [OpenAIRE] [PubMed] [DOI]

RepeatMasker Web site.

NCBI BLAST web site.

Johnson, M, Zaretskaya, I, Raytselis, Y, Merezhuk, Y, McGinnis, S, Madden, T. NCBI BLAST: a better web interface. Nucleic Acids Res. 2008; 36 (Web Server issue): W5-9 [OpenAIRE] [PubMed] [DOI]

Kent, W. BLAT--the BLAST-like alignment tool. Genome Res. 2002; 12 (4): 656-664 [OpenAIRE] [PubMed]

Cameron, M, Williams, H, Cannane, A. A deterministic finite automaton for faster protein hit detection in BLAST. J Comput Biol. 2006; 13 (4): 965-978 [OpenAIRE] [PubMed] [DOI]

NCBI C++ toolkit documentation.

26 references, page 1 of 2
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