ArticleGenomics, proteomics & bioinformatics2006
Fragrep: an efficient search tool for fragmented patterns in genomic sequences.
Article in Genomics, proteomics & bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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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.
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Who cites it
11 citing papers in PubMed.
- Inverse folding based pre-training for the reliable identification of intrinsic transcription terminators.PLoS computational biology · 2022Article
- Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas.Genome research · 2021Article
- Role ofFrontiers in cellular and infection microbiology · 2021Article
- The functional requirement of two structural domains within telomerase RNA emerged early in eukaryotes.Nucleic acids research · 2016Article
- Structure and function of echinoderm telomerase RNA.RNA (New York, N.Y.) · 2016Article
- pRNA: NoRC-associated RNA of rRNA operons.RNA biology · 2014Article
- maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences.Bioinformatics (Oxford, England) · 2011Article
- U7 snRNAs: a computational survey.Genomics, proteomics & bioinformatics · 2007Article
- Evolution of the vertebrate Y RNA cluster.Theory in biosciences = Theorie in den Biowissenschaften · 2007Article
- Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum.Current genetics · 2007Review
- Evolutionary patterns of non-coding RNAs.Theory in biosciences = Theorie in den Biowissenschaften · 2005Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many classes of non-coding RNAs (ncRNAs; including Y RNAs, vault RNAs, RNase P RNAs, and MRP RNAs, as well as a novel class recently discovered in Dictyostelium discoideum) can be characterized by a pattern of short but well-conserved sequence elements that are separated by poorly conserved regions of sometimes highly variable lengths. Local alignment algorithms such as BLAST are therefore ill-suited for the discovery of new homologs of such ncRNAs in genomic sequences. The Fragrep tool instead implements an efficient algorithm for detecting the pattern fragments that occur in a given order. For each pattern fragment, the mismatch tolerance and bounds on the length of the intervening sequences can be specified separately. Furthermore, matches can be ranked by a statistically well-motivated scoring scheme.
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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.