ArticleBMC bioinformatics2005
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed, 36 citations in OpenAlex.
- Transcription of microRNAs is regulated by developmental signaling pathways and transcription factors.Frontiers in cell and developmental biology · 2024Article
- Do echinoderm genomes measure up?Marine genomics · 2015Review
- Cis-regulatory control of the nuclear receptor Coup-TF gene in the sea urchin Paracentrotus lividus embryo.PloS one · 2014Article
- Developmental cis-regulatory analysis of the cyclin D gene in the sea urchin Strongylocentrotus purpuratus.Biochemical and biophysical research communications · 2013Article
- Cis-regulatory logic driving glial cells missing: self-sustaining circuitry in later embryogenesis.Developmental biology · 2012Article
- In silico characterization of the neural alpha tubulin gene promoter of the sea urchin embryo Paracentrotus lividus by phylogenetic footprinting.Molecular biology reports · 2012Article
- Article
- Information processing at the foxa node of the sea urchin endomesoderm specification network.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Functional cis-regulatory genomics for systems biology.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers.PLoS genetics · 2010Article
- Characterizing the transcriptional regulation of let-721, a Caenorhabditis elegans homolog of human electron flavoprotein dehydrogenase.Molecular genetics and genomics : MGG · 2009Article
- MOODS: fast search for position weight matrix matches in DNA sequences.Bioinformatics (Oxford, England) · 2009Article
- Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila.PLoS genetics · 2009Article
- Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence.Developmental biology · 2009Article
- A spatially dynamic cohort of regulatory genes in the endomesodermal gene network of the sea urchin embryo.Developmental biology · 2008Article
- The evolutionary origin of nodal-related genes in teleosts.Development genes and evolution · 2007Article
- Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network.Developmental biology · 2007Article
- Using genomics to study legume seed development.Plant physiology · 2007Review
- Selective constraint on noncoding regions of hominid genomes.PLoS computational biology · 2005Article
- An evolutionary constraint: strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundComparative sequence analysis is an effective and increasingly common way to identify cis-regulatory regions in animal genomes.
resultsWe describe three tools for comparative analysis of pairs of BAC-sized genomic regions. Paircomp is a tool that does windowed (ungapped) comparisons of two sequences and reports all matches above a set threshold. FamilyRelationsII is a graphical viewer for comparisons that enables interactive exploration of several different kinds of comparisons. Cartwheel is a Web site and compute-cluster management system used to execute and store comparisons for display by FamilyRelationsII. These tools are specialized for the discovery of cis-regulatory regions in animal genomes. All tools and their source code are freely available at http://family.caltech.edu/.
conclusionThese tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes.
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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.