Literature DB >> 21243090

Comparison of Current BLAST Software on Nucleotide Sequences.

I Elizabeth Cha1, Eric C Rouchka.   

Abstract

The computational power needed for searching exponentially growing databases, such as GenBank, has increased dramatically. Three different implementations of the most widely used sequence alignment tool, known as BLAST (Basic Local Alignment Search Tool), are studied for their efficiency on nucleotide-nucleotide comparisons. The performance of these implementations are evaluated using target databases and query sequences of varying lengths and number of entries constructed from human genomic and EST sequences. In general, WU BLAST was found to be most efficient when the database and query composition are unknown. NCBI BLAST appears to work best when the database contains a small number of sequences, while mpiBLAST shows the power of database distribution when the number of bases per target database is large. The optimal number of compute nodes in mpiBLAST varies depending upon the database, yet in the cases studied, remains surprisingly low.

Entities:  

Year:  2005        PMID： 21243090      PMCID： PMC3021256          DOI： 10.1109/IPDPS.2005.145

Source DB:  PubMed          Journal:  IPDPS


  14 in total

1.  BLAT--the BLAST-like alignment tool.

Authors:  W James Kent
Journal:  Genome Res       Date:  2002-04       Impact factor: 9.043

2.  Fast algorithms for large-scale genome alignment and comparison.

Authors:  Arthur L Delcher; Adam Phillippy; Jane Carlton; Steven L Salzberg
Journal:  Nucleic Acids Res       Date:  2002-06-01       Impact factor: 16.971

3.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

4.  Protein sequence similarity searches using patterns as seeds.

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Journal:  Nucleic Acids Res       Date:  1998-09-01       Impact factor: 16.971

5.  Rapid and sensitive protein similarity searches.

Authors:  D J Lipman; W R Pearson
Journal:  Science       Date:  1985-03-22       Impact factor: 47.728

6.  Improved tools for biological sequence comparison.

Authors:  W R Pearson; D J Lipman
Journal:  Proc Natl Acad Sci U S A       Date:  1988-04       Impact factor: 11.205

7.  A general method applicable to the search for similarities in the amino acid sequence of two proteins.

Authors:  S B Needleman; C D Wunsch
Journal:  J Mol Biol       Date:  1970-03       Impact factor: 5.469

8.  dbEST--database for "expressed sequence tags".

Authors:  M S Boguski; T M Lowe; C M Tolstoshev
Journal:  Nat Genet       Date:  1993-08       Impact factor: 38.330

9.  The turning point in genome research.

Authors:  M S Boguski
Journal:  Trends Biochem Sci       Date:  1995-08       Impact factor: 13.807

10.  The genome sequence and structure of rice chromosome 1.

Authors:  Takuji Sasaki; Takashi Matsumoto; Kimiko Yamamoto; Katsumi Sakata; Tomoya Baba; Yuichi Katayose; Jianzhong Wu; Yoshihito Niimura; Zhukuan Cheng; Yoshiaki Nagamura; Baltazar A Antonio; Hiroyuki Kanamori; Satomi Hosokawa; Masatoshi Masukawa; Koji Arikawa; Yoshino Chiden; Mika Hayashi; Masako Okamoto; Tsuyu Ando; Hiroyoshi Aoki; Kohei Arita; Masao Hamada; Chizuko Harada; Saori Hijishita; Mikiko Honda; Yoko Ichikawa; Atsuko Idonuma; Masumi Iijima; Michiko Ikeda; Maiko Ikeno; Sachie Ito; Tomoko Ito; Yuichi Ito; Yukiyo Ito; Aki Iwabuchi; Kozue Kamiya; Wataru Karasawa; Satoshi Katagiri; Ari Kikuta; Noriko Kobayashi; Izumi Kono; Kayo Machita; Tomoko Maehara; Hiroshi Mizuno; Tatsumi Mizubayashi; Yoshiyuki Mukai; Hideki Nagasaki; Marina Nakashima; Yuko Nakama; Yumi Nakamichi; Mari Nakamura; Nobukazu Namiki; Manami Negishi; Isamu Ohta; Nozomi Ono; Shoko Saji; Kumiko Sakai; Michie Shibata; Takanori Shimokawa; Ayahiko Shomura; Jianyu Song; Yuka Takazaki; Kimihiro Terasawa; Kumiko Tsuji; Kazunori Waki; Harumi Yamagata; Hiroko Yamane; Shoji Yoshiki; Rie Yoshihara; Kazuko Yukawa; Huisun Zhong; Hisakazu Iwama; Toshinori Endo; Hidetaka Ito; Jang Ho Hahn; Ho-Il Kim; Moo-Young Eun; Masahiro Yano; Jiming Jiang; Takashi Gojobori
Journal:  Nature       Date:  2002-11-21       Impact factor: 49.962
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  6 in total

1.  Genome-wide analysis of the heat shock transcription factors in Populus trichocarpa and Medicago truncatula.

Authors:  Fangming Wang; Qing Dong; Haiyang Jiang; Suwen Zhu; Beijiu Chen; Yan Xiang
Journal:  Mol Biol Rep       Date:  2011-05-29       Impact factor: 2.316

2.  Comparative in silico characterization of Klebsiella pneumoniae hypervirulent plasmids and their antimicrobial resistance genes.

Authors:  Negin Bolourchi; Anam Naz; Maryam Sohrabi; Farzad Badmasti
Journal:  Ann Clin Microbiol Antimicrob       Date:  2022-06-02       Impact factor: 6.781

3.  Novel domain combinations in proteins encoded by chimeric transcripts.

Authors:  Milana Frenkel-Morgenstern; Alfonso Valencia
Journal:  Bioinformatics       Date:  2012-06-15       Impact factor: 6.937

4.  A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus.

Authors:  Biao Tang; Feng Xie; Wei Zhao; Jian Wang; Shengwang Dai; Huajun Zheng; Xiaoming Ding; Xufeng Cen; Haican Liu; Yucong Yu; Haokui Zhou; Yan Zhou; Lixin Zhang; Michael Goodfellow; Guo-Ping Zhao
Journal:  Synth Syst Biotechnol       Date:  2016-09-01

5.  The Complete Mitogenome of Elymus sibiricus and Insights Into Its Evolutionary Pattern Based on Simple Repeat Sequences of Seed Plant Mitogenomes.

Authors:  Yanli Xiong; Qingqing Yu; Yi Xiong; Junming Zhao; Xiong Lei; Lin Liu; Wei Liu; Yan Peng; Jianbo Zhang; Daxu Li; Shiqie Bai; Xiao Ma
Journal:  Front Plant Sci       Date:  2022-01-26       Impact factor: 5.753

6.  Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

Authors:  Milana Frenkel-Morgenstern; Vincent Lacroix; Iakes Ezkurdia; Yishai Levin; Alexandra Gabashvili; Jaime Prilusky; Angela Del Pozo; Michael Tress; Rory Johnson; Roderic Guigo; Alfonso Valencia
Journal:  Genome Res       Date:  2012-05-15       Impact factor: 9.043
  6 in total

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