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Basic Local Alignment Search Tool

Published on Oct 1, 1990in Journal of Molecular Biology 4.89
· DOI :10.1016/S0022-2836(05)80360-2
Stephen F. Altschul46
Estimated H-index: 46
(National Institutes of Health),
Warren Gish15
Estimated H-index: 15
(National Institutes of Health)
+ 2 AuthorsDavid J. Lipman45
Estimated H-index: 45
(National Institutes of Health)
Abstract
A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straight-forward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
  • References (23)
  • Citations (59945)
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References23
Newest
Published on Sep 1, 1997in Nucleic Acids Research 11.56
Stephen F. Altschul46
Estimated H-index: 46
,
Thomas L. Madden20
Estimated H-index: 20
+ 4 AuthorsDavid J. Lipman45
Estimated H-index: 45
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. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST progr...
57.5k Citations Source Cite
Published on Jun 1, 1991in Journal of Molecular Biology 4.89
Stephen F. Altschul46
Estimated H-index: 46
(National Institutes of Health)
Protein sequence alignments have become an important tool for molecular biologists. Local alignments are frequently constructed with the aid of a "substitution score matrix" that specifies a score for aligning each pair of amino acid residues. Over the years, many different substitution matrices have been proposed, based on a wide variety of rationales. Statistical results, however, demonstrate that any such matrix is i.mplicitly a "log-odds" matrix, with a specific target distribution for align...
557 Citations Source Cite
Published on Jun 1, 1990in Annals of Statistics 2.52
Samuel Karlin78
Estimated H-index: 78
,
Amir Dembo36
Estimated H-index: 36
,
Tsutomu Kawabata10
Estimated H-index: 10
A method and system for generating signals indicative of data concerning environmental characteristics. A detector is provided incorporating a plurality of detecting elements, each having a predetermined threshold level and thus selectively capable of providing a sensible indication of the presence of an environmental characteristic of magnitude equal to or greater than such threshold level. The detecting elements are correlated in respect of their threshold levels with a preselected numerical s...
89 Citations Source Cite
S Karlin2
Estimated H-index: 2
,
Stephen F. Altschul46
Estimated H-index: 46
An unusual pattern in a nucleic acid or protein sequence or a region of strong similarity shared by two or more sequences may have biological significance. It is therefore desirable to know whether such a pattern can have arisen simply by chance. To identify interesting sequence patterns, appropriate scoring values can be assigned to the individual residues of a single sequence or to sets of residues when several sequences are compared. For single sequences, such scores can reflect biophysical p...
1,566 Citations Source Cite
Randall F. Smith2
Estimated H-index: 2
,
Temple F. Smith37
Estimated H-index: 37
Abstract We have developed a computer algorithm that can extract the pattern of conserved primary sequence elements common to all members of a homologous protein family. The method involves clustering the pairwise similarity scores among a set of related sequences to generate a binary dendrogram (tree). The tree is then reduced in a stepwise manner by progressively replacing the node connecting the two most similar termini by one common pattern until only a single common "root" pattern remains. ...
232 Citations Source Cite
Published on Jan 1, 1989in Journal of Molecular Biology 4.89
Jean B. Margot2
Estimated H-index: 2
(Pennsylvania State University),
G. William Demers3
Estimated H-index: 3
(Pennsylvania State University),
Ross C. Hardison67
Estimated H-index: 67
(Pennsylvania State University)
Abstract The nucleotide sequence of the entire β-like globin gene cluster of rabbits has been determined. This sequence of a continuous stretch of 44.5 × 10 3 base-pairs (bp) starts about 6 × 10 3 bp upstream from e (the 5′-most gene) and ends about 12 × 10 3 bp downstream from β (the 3′-most gene). Analysis of the sequence reveals that: (1) the sequence is relatively A + T rich (about 60%); (2) regions with high G + C content are associated with OcC repeats, a short interspersed repeated DNA in...
59 Citations Source Cite
William R. Pearson46
Estimated H-index: 46
,
David J. Lipman45
Estimated H-index: 45
We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an ...
9,978 Citations Source Cite
Published on Oct 1, 1987in The Computer Journal 0.79
A. F. W. Coulson2
Estimated H-index: 2
(University of Edinburgh),
J. F. Collins2
Estimated H-index: 2
(University of Edinburgh),
Andrew Lyall6
Estimated H-index: 6
(University of Edinburgh)
Sequence analysis of protein and nucleic acid databases by exhaustive string-matching algorithms is effectively implemented on large processor-array machines, such as the I.C.L. DAP. An improved method of assessing the significance of the best alignments for proteins is described. Examples involving the cystic fibrosis antigen and Drosophila vitellogenins illustrate the usefulness of this approach.
75 Citations Source Cite
Published on Jan 1, 1986in Nucleic Acids Research 11.56
Osamu Gotoh47
Estimated H-index: 47
,
Yusaku Tagashira14
Estimated H-index: 14
Abstract A set of programs was developed for searching nucleic acid and protein sequence data bases for sequences similar to a given sequence. The programs, written in FORTRAN 77, were optimized for vector processing on a Hitachi S810-20 supercomputer. A search of a 500-residue protein sequence against the entire PIR data base Ver. 1.0 (1) (0.5 M residues) is carried out in a CPU time of 45 sec. About 4 min is required for an exhaustive search of a 1500-base nucleotide sequence against all mamma...
10 Citations Source Cite
Published on Mar 22, 1985in Science 41.06
David J. Lipman45
Estimated H-index: 45
,
William R. Pearson46
Estimated H-index: 46
An algorithm was developed which facilitates the search for similarities between newly determined amino acid sequences and sequences already available in databases. Because of the algorithm9s efficiency on many microcomputers, sensitive protein database searches may now become a routine procedure for molecular biologists. The method efficiently identifies regions of similar sequence and then scores the aligned identical and differing residues in those regions by means of an amino acid replacabil...
2,746 Citations Source Cite
Cited By59945
Newest
Published on May 24, 2019in Artificial Cells Nanomedicine and Biotechnology 3.03
Suriya Rehman2
Estimated H-index: 2
,
B. Rabindran Jermy2
Estimated H-index: 2
+ 7 AuthorsAdil Gani19
Estimated H-index: 19
(University of Kashmir)
AbstractThe establishment of a benign system for the nanoparticle (NPs) synthesis, is a key in nanotechnology for the environmental and health care industries. Therefore, enrichment of novel biological systems for the green synthesis is in significant demand, to lift up these compounds in the biomedical industries. The present work, reports the green synthesis of ZnO NPs, employing a novel thermophile, identified as Bacillus haynesii (GeneBank: MG822851) isolated from the leaf of date palm plant...
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Published on Apr 24, 2019in BMC Genomics 3.73
Manuel Bernabeu1
Estimated H-index: 1
(University of Barcelona),
José Francisco Sánchez-Herrero1
Estimated H-index: 1
(University of Barcelona)
+ 4 AuthorsAntonio Juárez30
Estimated H-index: 30
(University of Barcelona)
Background Gene duplication underlies a significant proportion of gene functional diversity and genome complexity in both eukaryotes and prokaryotes. Although several reports in the literature described the duplication of specific genes in E. coli, a detailed analysis of the extent of gene duplications in this microorganism is needed.
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Published on Mar 11, 2019in BMC Genomics 3.73
María Carla Piazzon2
Estimated H-index: 2
(Spanish National Research Council),
Ivona Mladineo13
Estimated H-index: 13
+ 6 AuthorsAriadna Sitjà-Bobadilla33
Estimated H-index: 33
(Spanish National Research Council)
Background Monogenean flatworms are the main fish ectoparasites inflicting serious economic losses in aquaculture. The polyopisthocotylean Sparicotyle chrysophrii parasitizes the gills of gilthead sea bream (GSB, Sparus aurata) causing anaemia, lamellae fusion and sloughing of epithelial cells, with the consequent hypoxia, emaciation, lethargy and mortality. Currently no preventive or curative measures against this disease exist and therefore information on the host-parasite interaction is cruci...
1 Citations Source Cite
Published on Mar 1, 2019in Scientific Reports 4.12
Mitra Kabir1
Estimated H-index: 1
(Manchester Academic Health Science Centre),
Stephanie Wenlock (University of Cambridge)+ 1 AuthorsKathryn E. Hentges13
Estimated H-index: 13
(Manchester Academic Health Science Centre)
During the evolution of multicellular eukaryotes, gene duplication occurs frequently to generate new genes and/or functions. A duplicated gene may have a similar function to its ancestral gene. Therefore, it may be expected that duplicated genes are less likely to be critical for the survival of an organism, since there are multiple copies of the gene rendering each individual copy redundant. In this study, we explored the developmental expression patterns of duplicate gene pairs and the relatio...
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Published on Feb 22, 2019in Scientific Reports 4.12
Sílvio Roberto Branco Santos12
Estimated H-index: 12
(University of Minho),
A. Oliveira8
Estimated H-index: 8
(University of Minho)
+ 1 AuthorsJoana Azeredo47
Estimated H-index: 47
(University of Minho)
Bacteriophage endolysins present enormous biotechnological potentials and have been successfully used to control and detect bacterial pathogens. Endolysins targeting Gram-positive bacteria are modular, displaying a cell binding (CBD) and an enzymatically active domain. The CBD of phage endolysins are recognized by their high specificity and host affinity, characteristics that make them promising diagnostic tools. No CBD able to bind Paenibacillus larvae has been identified so far. P. larvae is a...
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Published on Jan 3, 2019in Mobile Dna 5.89
Pavel Neumann27
Estimated H-index: 27
,
Petr Novák48
Estimated H-index: 48
+ 1 AuthorsJiří Macas32
Estimated H-index: 32
Background Plant LTR-retrotransposons are classified into two superfamilies, Ty1/copia and Ty3/gypsy. They are further divided into an enormous number of families which are, due to the high diversity of their nucleotide sequences, usually specific to a single or a group of closely related species. Previous attempts to group these families into broader categories reflecting their phylogenetic relationships were limited either to analyzing a narrow range of plant species or to analyzing a small nu...
3 Citations Source Cite
Published on Mar 1, 2019in BMC Biology 5.77
Courtney W. Stairs (Uppsala University), Anna Kokla (Swedish University of Agricultural Sciences)+ 3 AuthorsThijs J. G. Ettema31
Estimated H-index: 31
(Uppsala University)
BACKGROUND: Spironucleus salmonicida is an anaerobic parasite that can cause systemic infections in Atlantic salmon. Unlike other diplomonad parasites, such as the human pathogen Giardia intestinalis, Spironucleus species can infiltrate the blood stream of their hosts eventually colonizing organs, skin and gills. How this presumed anaerobe can persist and invade oxygenated tissues, despite having a strictly anaerobic metabolism, remains elusive. RESULTS: To investigate how S. salmonicida respons...
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Published on Mar 7, 2019in Nutrition Journal 3.57
Akemi T. Wijayabahu (University of Florida), Sheldon Waugh4
Estimated H-index: 4
(University of Florida)
+ 1 AuthorsVolker Mai29
Estimated H-index: 29
(University of Florida)
Background Dried fruits, such as raisins, contain phytochemicals and dietary fibers that contribute to maintaining health, potentially at least partially through modification in gut microbiota composition and activities. However, the effects of raisin consumption on gut microbiota have not previously been thoroughly investigated in humans. Therefore, the objective of this study was to determine how adding three servings of sun dried raisin/day to the diet of healthy volunteers affects gut microb...
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Published on May 8, 2019in BMC Evolutionary Biology 3.03
Danang Crysnanto (ETH Zurich), Darren J. Obbard25
Estimated H-index: 25
(University of Edinburgh)
RNA interference (RNAi) related pathways provide defense against viruses and transposable elements, and have been implicated in the suppression of meiotic drive elements. Genes in these pathways often exhibit high levels of adaptive substitution, and over longer timescales show frequent gene duplication and loss-most likely as a consequence of their role in mediating conflict with these parasites. This is particularly striking for Argonaute 2 (Ago2), which is ancestrally the key effector of anti...
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Published on Mar 14, 2019in BMC Bioinformatics 2.21
Qingchen Zhang5
Estimated H-index: 5
(Tongji University),
Lu Zhang (Tongji University)+ 5 AuthorsZhiwei Cao21
Estimated H-index: 21
(Tongji University)
Background Functional antibody genes are often assembled by VDJ recombination and then diversified by somatic hypermutation. Identifying the combination of sourcing germline genes is critical to understand the process of antibody maturation, which may facilitate the diagnostics and rapid generation of human monoclonal antibodies in therapeutics. Despite of successful efforts in V and J fragment assignment, method in D segment tracing remains weak for immunoglobulin heavy diversity (IGHD).
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