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Literature DB >> 15215342

BLAST: at the core of a powerful and diverse set of sequence analysis tools.

Abstract

Basic Local Alignment Search Tool (BLAST) is one of the most heavily used sequence analysis tools available in the public domain. There is now a wide choice of BLAST algorithms that can be used to search many different sequence databases via the BLAST web pages (http://www.ncbi.nlm.nih.gov/BLAST/). All the algorithm-database combinations can be executed with default parameters or with customized settings, and the results can be viewed in a variety of ways. A new online resource, the BLAST Program Selection Guide, has been created to assist in the definition of search strategies. This article discusses optimal search strategies and highlights some BLAST features that can make your searches more powerful.

Mesh：

Substances：
Nucleotides

Year: 2004 PMID： 15215342 PMCID： PMC441573 DOI： 10.1093/nar/gkh435

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

11 in total

1. A greedy algorithm for aligning DNA sequences.

Authors: Z Zhang; S Schwartz; L Wagner; W Miller
Journal: J Comput Biol Date: 2000 Feb-Apr Impact factor: 1.479

2. CDD: a database of conserved domain alignments with links to domain three-dimensional structure.

Authors: Aron Marchler-Bauer; Anna R Panchenko; Benjamin A Shoemaker; Paul A Thiessen; Lewis Y Geer; Stephen H Bryant
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

3. PatternHunter: faster and more sensitive homology search.

Authors: Bin Ma; John Tromp; Ming Li
Journal: Bioinformatics Date: 2002-03 Impact factor: 6.937

4. Efficient large-scale sequence comparison by locality-sensitive hashing.

Authors: J Buhler
Journal: Bioinformatics Date: 2001-05 Impact factor: 6.937

5. Protein sequence similarity searches using patterns as seeds.

Authors: Z Zhang; A A Schäffer; W Miller; T L Madden; D J Lipman; E V Koonin; S F Altschul
Journal: Nucleic Acids Res Date: 1998-09-01 Impact factor: 16.971

Review 6. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors: S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal: Nucleic Acids Res Date: 1997-09-01 Impact factor: 16.971

7. Positional cloning of the gene for multiple endocrine neoplasia-type 1.

Authors: S C Chandrasekharappa; S C Guru; P Manickam; S E Olufemi; F S Collins; M R Emmert-Buck; L V Debelenko; Z Zhuang; I A Lubensky; L A Liotta; J S Crabtree; Y Wang; B A Roe; J Weisemann; M S Boguski; S K Agarwal; M B Kester; Y S Kim; C Heppner; Q Dong; A M Spiegel; A L Burns; S J Marx
Journal: Science Date: 1997-04-18 Impact factor: 47.728

8. Analysis of expressed sequence tags (EST) obtained from common carp, Cyprinus carpio L., head kidney cells after stimulation by two mitogens, lipopolysaccharide and concanavalin-A.

Authors: Ram Savan; Masahiro Sakai
Journal: Comp Biochem Physiol B Biochem Mol Biol Date: 2002-01 Impact factor: 2.231

9. Human choroideremia protein contains a FAD-binding domain.

Authors: E V Koonin
Journal: Nat Genet Date: 1996-03 Impact factor: 38.330

10. Amino acid substitution matrices from an information theoretic perspective.

Authors: S F Altschul
Journal: J Mol Biol Date: 1991-06-05 Impact factor: 5.469

540 in total

1. Fungi and animals may share a common ancestor to nuclear receptors.

Authors: Chris Phelps; Valentina Gburcik; Elena Suslova; Peter Dudek; Fedor Forafonov; Nathalie Bot; Morag MacLean; Richard J Fagan; Didier Picard
Journal: Proc Natl Acad Sci U S A Date: 2006-04-24 Impact factor: 11.205

2. Complete genome sequence of the giant virus OBP and comparative genome analysis of the diverse ΦKZ-related phages.

Authors: Anneleen Cornelissen; Stephen C Hardies; Olga V Shaburova; Victor N Krylov; Wesley Mattheus; Andrew M Kropinski; Rob Lavigne
Journal: J Virol Date: 2011-11-30 Impact factor: 5.103

3. Novel plasmid and its variant harboring both a bla(NDM-1) gene and type IV secretion system in clinical isolates of Acinetobacter lwoffii.

Authors: Hongyan Hu; Yongfei Hu; Yuanlong Pan; Hui Liang; Haiyan Wang; Xiumei Wang; Qinfang Hao; Xiaoli Yang; Xi Yang; Xue Xiao; Chunguang Luan; Yi Yang; Yujun Cui; Ruifu Yang; George F Gao; Yajun Song; Baoli Zhu
Journal: Antimicrob Agents Chemother Date: 2012-01-30 Impact factor: 5.191

BLAST: at the core of a powerful and diverse set of sequence analysis tools.

1. A greedy algorithm for aligning DNA sequences.

2. CDD: a database of conserved domain alignments with links to domain three-dimensional structure.

3. PatternHunter: faster and more sensitive homology search.

4. Efficient large-scale sequence comparison by locality-sensitive hashing.

5. Protein sequence similarity searches using patterns as seeds.

Review 6. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

7. Positional cloning of the gene for multiple endocrine neoplasia-type 1.

8. Analysis of expressed sequence tags (EST) obtained from common carp, Cyprinus carpio L., head kidney cells after stimulation by two mitogens, lipopolysaccharide and concanavalin-A.

9. Human choroideremia protein contains a FAD-binding domain.

10. Amino acid substitution matrices from an information theoretic perspective.

1. Fungi and animals may share a common ancestor to nuclear receptors.

2. Complete genome sequence of the giant virus OBP and comparative genome analysis of the diverse ΦKZ-related phages.

3. Novel plasmid and its variant harboring both a bla(NDM-1) gene and type IV secretion system in clinical isolates of Acinetobacter lwoffii.

Review 4. PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas species.

5. Bordetella avium antibiotic resistance, novel enrichment culture, and antigenic characterization.

6. Characterisation of PfRON6, a Plasmodium falciparum rhoptry neck protein with a novel cysteine-rich domain.

7. Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.

8. Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans.

Review 9. Towards the automatic classification of neurons.

10. Spatial and temporal expression of Lactobacillus plantarum genes in the gastrointestinal tracts of mice.