Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST

Abstract

TBLASTN is widely used, as it is common to wish to compare proteins to chromosomes or to libraries of mRNAs. Composition-based statistics improve the statistical accuracy, and therefore the reliability, of TBLASTN results. The algorithms used by TBLASTN are not widely known, and some of the most important are reported here. The data used to test TBLASTN are available for download and may be useful in other studies of translated search algorithms.

Keywords

Composition (language)Computer scienceInformation retrievalStatisticsBiologyData miningComputational biologyDatabaseMathematics

Affiliated Institutions

National Institutes of Health US

Related Publications

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

Jasmine Chong , Othman Soufan , Carin Li +5 more

We present a new update to MetaboAnalyst (version 4.0) for comprehensive metabolomic data analysis, interpretation, and integration with other omics data. Since the last major u...

2018 Nucleic Acids Research 3661 citations

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

Stephen F. Altschul

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 s...

1997 Nucleic Acids Research 73388 citations

Search and clustering orders of magnitude faster than BLAST

R. C. Edgar

Abstract Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. Results: UBLAS...

2010 Bioinformatics 20899 citations

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights

Zhiqiang Pang , Jasmine Chong , Guangyan Zhou +7 more

Abstract Since its first release over a decade ago, the MetaboAnalyst web-based platform has become widely used for comprehensive metabolomics data analysis and interpretation. ...

2021 Nucleic Acids Research 3857 citations

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

Nicholas A. Bokulich , Benjamin D. Kaehler , Jai Ram Rideout +5 more

2018 Microbiome 5410 citations

Publication Info

Year: 2006
Type: article
Volume: 4
Issue: 1
Pages: 41-41
Citations: 581
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

581

OpenAlex

Cite This

APA Style

                            
                                
                                    E. Michael Gertz, 
                                
                                    Yi‐Kuo Yu, 
                                
                                    Richa Agarwala
                                
                                et al.
                            
                            (2006). 
                            Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST. 
                            BMC Biology
                            , 4
                            (1)
                            , 41-41.
                            https://doi.org/10.1186/1741-7007-4-41
                        

Identifiers

DOI: 10.1186/1741-7007-4-41