A new generation of protein database search programs

Gapped BLAST and PSI-BLAST: a new generation of protein ...

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9/1/1997 · Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. S F Altschul , T L Madden , A A Schäffer , J Zhang , Z Zhang , W Miller , and D J Lipman National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. altschul@ncbi.nlm.nih.gov

Gapped BLAST and PSI-BLAST: a new generation of protein ...

Gapped BLAST and PSI-BLAST: a new generation of protein ...

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Stephen F. Altschul*, Thomas L. Madden, Alejandro A. Schäffer 1, Jinghui Zhang, Zheng Zhang2, Webb Miller2 and David J. Lipman National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health,

Gapped BLAST and PSI-BLAST: a new generation of protein ...

Gapped BLAST and PSI-BLAST: a new generation of protein ...

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. @article{Altschul1997GappedBA, title=Gapped BLAST and PSI-BLAST: a new generation of protein database search programs., author=Stephen F. Altschul and Thomas L. Madden and Alejandro A. Sch\"affer and Jinghui Zhang and Zheng Zhang and Webb Miller and David J. Lipman, …

Gapped BLAST and PSI-BLAST: a new generation of protein ...

Gapped BLAST and PSI-BLAST: a new generation of protein ...

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The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities.

Gapped BLAST and PSI-BLAST: a new generation of protein ...

Protein Database | sci-wiz

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(2001) "Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements." Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005. PubMed. Park Y, Sheetlin S, Ma N, Madden TL, & Spouge JL. (2012) "New …

Protein Database | sci-wiz

BLAST PROGRAMS - BLAST: Basic Local Alignment Search Tool

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs (English)

BLAST PROGRAMS - BLAST: Basic Local Alignment Search Tool

Gapped BLAST and PSI-BLAST: a new generation of protein ...

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CiteSeerX - Scientific documents that cite the following paper: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research

Gapped BLAST and PSI-BLAST: a new generation of protein ...

Gapped BLAST and PSI-BLAST: a new generation of protein ...

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1: Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Gapped BLAST and PSI-BLAST: a new generation of protein ...

Gapped BLAST and PSI-BLAST: a new generation of protein ...

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In this work we use an open source software program called pClust to cluster proteins from the complete proteomes of twelve species of Alphaproteobacteria and generate a dendrogram from the resulting orthologous protein clusters.

Gapped BLAST and PSI-BLAST: a new generation of protein ...

Altschul, S.F.; Madden, T.L.; Schaffer, A.A.; Zhang, J ...

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28 rows · This list of sequence alignment software is a compilation of software tools and web portals …

Altschul, S.F.; Madden, T.L.; Schaffer, A.A.; Zhang, J ...

List of sequence alignment software - Wikipedia

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For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating ...

List of sequence alignment software - Wikipedia

Gapped Blast and PsiBlast: a new generation of protein ...

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PSIBLAST can repeatedly search the target databases, using a multiple alignment of high scoring sequences found in each search round to generate a new PSSM for use in the next round of searching. PSIBLAST will iterate until no new sequences are found, or the user specified maximum number of iterations is reached, whichever comes first.

Gapped Blast and PsiBlast: a new generation of protein ...

PSIBLAST - Department of Biology

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Particularly, we propose a method for generation of features based on sequence motifs and those features are firstly employed in protein fold prediction. PFP-RFSM and ten representative protein fold predictors are validated in a benchmark dataset consisting of 27 fold types.

PSIBLAST - Department of Biology

NCBI reference sequences (RefSeq): a curated non-redundant ...

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one extension is invoked per 50 database sequences • The resulting gapped alignment is reported only if it has an E-value low enough to be of interest Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a New Generation of Protein Database Search Programs. Nucleic Acids Res., 25(17):3389 ...

NCBI reference sequences (RefSeq): a curated non-redundant ...

Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J ...

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8/25/2014 · Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. By Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch ä ffer, Jinghui Zhang, Zheng Zhang, Webb Miller and David J. Lipman. Introduction to BLAST. Slideshow 3547272 by lamar

Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J ...

Algorithms for Sequence Alignment - Donald Bren School of ...

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Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (2004).Gapped BLAST and PSI-BLAST: A new generation of protein database …

Algorithms for Sequence Alignment - Donald Bren School of ...

Gapped BLAST and PSI-BLAST: a new generation of protein ...

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. has been cited by the following article: Article. Evaluation and Analysis of Bacterial Communities from Different Waste Water Treatment Plants by Denaturing Gradient Gel Electrophoresis with Group Specific 16s rRNA.

Gapped BLAST and PSI-BLAST: a new generation of protein ...

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z ...

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Programs search protein databases using a protein query. Algorithms: blastp, psi-blast, phi-blast, delta-blast.

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z ...

Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z ...

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A Shaffer's 1 research works with 27,736 citations and 208 reads, including: Gapped blast and psi-blast:A new generation of protein database search programs. A Shaffer has expertise in Biology and ...

Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z ...

BLASTP - omicX

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PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. RID: GA9THX23015 Database: chicken build 2 version 1 protein database 18,529 sequences; 8,732,257 total letters Query= Length=150 Distribution of 3 Blast Hits on the Query Sequence

BLASTP - omicX

A Shaffer's research works in Biology and Computer Science

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single NREF entry with protein IDs, accession numbers, and protein names from each underlying database, as well as amino acid sequence, taxonomy, and composite bibliographic data. Also listed are related sequences identified by all-against-all FASTA search (6), …

A Shaffer's research works in Biology and Computer Science

PSI BLAST a new generation of protein database search ...

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J. Lipman's 1 research works with 562 citations and 236 reads, including: A new generation of protein database search programs. J. Lipman has expertise in Medicine and Social Science.

PSI BLAST a new generation of protein database search ...

TheProteinInformationResource

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BLAST 2.2.27 Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic …

TheProteinInformationResource
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