ArticleBMC biology2006
Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST.
Article in BMC biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 366 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
366 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Chromosome-level genome and transcriptome analysis ofVirulence · 2026Article
- Investigation of colistin-resistant non-humanMicrobiology spectrum · 2026Article
- Computational Design of a Trivalent Multi-Epitope mRNA Vaccine Candidate Against Western, Eastern, and Venezuelan Equine Encephalitis Viruses.Pharmaceutical research · 2026Article
- Pyridoxal-phosphate-dependent biosynthesis of aminovaleramide by AvaS in tRNA.Nature chemical biology · 2026Article
- Reference-Guided Chromosome-Scale Genome Assembly With Insights on Population Genomics of the Atlantic Goliath Grouper (Ecology and evolution · 2026Article
- Chromosome-scale assembly of the eliteHorticulture research · 2026Article
- Article
- Identification and Characterization of Genes Associated With Wood Property Traits via Genome Sequencing in Fast-Growing Species of GenusEvolutionary applications · 2026Article
- Functional conservation of IR75q.2 in the recognition of volatile acids and aldehydes in two Spodoptera species.Crop health · 2026Article
- Chromosome-scale genome of Myriophyllum spicatum unveils the role of allohexaploidy in driving aquatic adaptation and widespread invasion.The Plant journal : for cell and molecular biology · 2026Article
- Evolutionary History of the α-Carbonic Anhydrase Gene Family in the Phylum Arthropoda, With Comparisons to αCA in Chordates.Genome biology and evolution · 2026Article
- Divergent Evolutionary Profile ofAnimals : an open access journal from MDPI · 2026Article
- A near telomere-to-telomere genome assembly of the tobacco root rot pathogen Fusarium oxysporum.Scientific data · 2026Article
- An invariant VLR-like receptor refines the T-like cell framework in lamprey.Nature communications · 2026Article
- Reproductive mode and ploidy are associated with distinct organization of clustered centromeric regions in Meloidogyne nematodes.Genome biology · 2026Article
- Whole-genome analyses illuminate demographic history and lineage differentiation of polymorphic swallowtail butterfly Papilio bootes.BMC genomics · 2026Article
- Chromosome-level genome assembly of Xuefeng Black-bone chicken and comparative genomics analysis.BMC genomics · 2026Article
- A chromosome-level genome assembly of the Tristram's Bunting (Emberiza tristrami).Scientific data · 2026Article
- Transition From Land to Sea: Comparative Genomics Illuminates the Adaptive Evolution of the Intertidal Spider.Molecular ecology resources · 2026Article
306 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
backgroundTBLASTN is a mode of operation for BLAST that aligns protein sequences to a nucleotide database translated in all six frames. We present the first description of the modern implementation of TBLASTN, focusing on new techniques that were used to implement composition-based statistics for translated nucleotide searches. Composition-based statistics use the composition of the sequences being aligned to generate more accurate E-values, which allows for a more accurate distinction between true and false matches. Until recently, composition-based statistics were available only for protein-protein searches. They are now available as a command line option for recent versions of TBLASTN and as an option for TBLASTN on the NCBI BLAST web server.
resultsWe evaluate the statistical and retrieval accuracy of the E-values reported by a baseline version of TBLASTN and by two variants that use different types of composition-based statistics. To test the statistical accuracy of TBLASTN, we ran 1000 searches using scrambled proteins from the mouse genome and a database of human chromosomes. To test retrieval accuracy, we modernize and adapt to translated searches a test set previously used to evaluate the retrieval accuracy of protein-protein searches. We show that composition-based statistics greatly improve the statistical accuracy of TBLASTN, at a small cost to the retrieval accuracy.
conclusionTBLASTN 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.