ArticleBioinformatics (Oxford, England)2011
Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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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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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.
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Who cites it
12 citing papers in PubMed.
- Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum).DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Detection ofFrontiers in molecular biosciences · 2021Article
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- Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations ofEvolutionary applications · 2018Article
- Range expansion underlies historical introgressive hybridization in the Iberian hare.Scientific reports · 2017Article
- Transcriptome analysis of root response to citrus blight based on the newly assembled Swingle citrumelo draft genome.BMC genomics · 2016Article
- Pathogen-regulated genes in wheat isogenic lines differing in resistance to brown rust Puccinia triticina.BMC genomics · 2015Article
- Article
- MEGANTE: a web-based system for integrated plant genome annotation.Plant & cell physiology · 2014Article
- Article
- Article
- HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies.Genome research · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
unlabelledThe large number of genomes that will be sequenced will need to be annotated with genes and other functional features. Aligning gene sequences from a related species to the target genome is an economical and highly reliable method to identify genes; unfortunately, existing tools have been lacking in sensitivity and speed. A program we reported, sim4cc, was shown to be highly accurate but is limited to comparing one cDNA with one genomic sequence. We present here an optimization of the tool, implemented in the packages sim4db and leaff. The new tool performs batch alignments of cDNA and genomic sequences in a fraction of the time required by its predecessor, and thus is very well suited for genome-wide analyses. AVAILABILITY: Sim4db and leaff are written in C, C++ and Perl for Linux and other Unix platforms. Source code is distributed free of charge from http://sourceforge.net/projects/kmer/. CONTACT: florea@umiacs.umd.edu
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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.