dbCNS: A New Database for Conserved Noncoding Sequences.

Molecular Biology and Evolution
Jun Inoue, Naruya Saitou

Abstract

We developed dbCNS (http://yamasati.nig.ac.jp/dbcns), a new database for conserved noncoding sequences (CNSs). CNSs exist in many eukaryotes and are assumed to be involved in protein expression control. Version 1 of dbCNS, introduced here, includes a powerful and precise CNS identification pipeline for multiple vertebrate genomes. Mutations in CNSs may induce morphological changes and cause genetic diseases. For this reason, many vertebrate CNSs have been identified, with special reference to primate genomes. We integrated ∼6.9 million CNSs from many vertebrate genomes into dbCNS, which allows users to extract CNSs near genes of interest using keyword searches. In addition to CNSs, dbCNS contains published genome sequences of 161 species. With purposeful taxonomic sampling of genomes, users can employ CNSs as queries to reconstruct CNS alignments and phylogenetic trees, to evaluate CNS modifications, acquisitions, and losses, and to roughly identify species with CNSs having accelerated substitution rates. dbCNS also produces links to dbSNP for searching pathogenic single-nucleotide polymorphisms in human CNSs. Thus, dbCNS connects morphological changes with genetic diseases. A test analysis using 38 gnathostome genomes was acco...Continue Reading

References

Apr 11, 1975·Science·M C King, A C Wilson
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Feb 28, 1995·Proceedings of the National Academy of Sciences of the United States of America·S AparicioS Brenner
Aug 26, 1999·Trends in Genetics : TIG·W J Gehring, K Ikeo
May 8, 2004·Science·Gill BejeranoDavid Haussler
Jun 25, 2004·Nucleic Acids Research·Kelly A FrazerInna Dubchak
Jul 19, 2005·Genome Research·Adam SiepelDavid Haussler
Oct 4, 2006·Developmental Biology·Dirk A KleinjanVeronica van Heyningen
Nov 30, 2006·Nucleic Acids Research·Axel ViselLen A Pennacchio
Dec 5, 2006·Nucleic Acids Research·R M KuhnW J Kent
May 10, 2007·Nucleic Acids Research·Michael BrudnoInna Dubchak
Oct 3, 2007·Development, Growth & Differentiation·Tadashi NomuraNoriko Osumi
Jun 10, 2009·Bioinformatics·Salvador Capella-GutiérrezToni Gabaldón
Feb 27, 2010·Bioinformatics·Matthieu MuffatoHugues Roest Crollius
Nov 18, 2010·Molecular Biology and Evolution·Alison P LeeByrappa Venkatesh
Dec 15, 2010·PLoS Computational Biology·Eugene V DavydovSerafim Batzoglou
Feb 1, 2011·Briefings in Bioinformatics·Melissa J HubiszAdam Siepel
Sep 24, 2011·Molecular Biology and Evolution·Kenta Sumiyama, Naruya Saitou
Apr 13, 2012·Bioinformatics·Andrei-Alin PopescuEmmanuel Paradis
Nov 30, 2012·Nucleic Acids Research·Slavica Dimitrieva, Philipp Bucher
Dec 26, 2012·Genome Biology and Evolution·Masatoshi Matsunami, Naruya Saitou
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Nov 22, 2013·Genome Biology and Evolution·Isaac Adeyemi Babarinde, Naruya Saitou
Dec 3, 2013·American Journal of Human Genetics·Shipra BhatiaDirk A Kleinjan
Jun 22, 2014·Genome Biology and Evolution·Nathalie FeinerShigehiro Kuraku
Nov 5, 2014·Genome Biology and Evolution·Nilmini HettiarachchiNaruya Saitou
May 28, 2015·Journal of Evolutionary Biology·B F SimõesD J Gower
Mar 28, 2016·Molecular Biology and Evolution·Isaac Adeyemi Babarinde, Naruya Saitou
Apr 30, 2016·Experimental Eye Research·Ales Cvekl, Patrick Callaerts
Jun 12, 2016·Genome Biology and Evolution·Morteza Mahmoudi SaberNaruya Saitou
Jan 4, 2017·Genome Biology and Evolution·Nilmini Hettiarachchi, Naruya Saitou
Nov 10, 2017·Nucleic Acids Research·Dimitris PolychronopoulosBoris Lenhard
Jan 27, 2018·Nature Communications·Filipe O Da SilvaNicolas Di-Poï
Nov 11, 2018·Nature Communications·Juliana G RoscitoMichael Hiller
Jun 14, 2019·Bioinformatics·Amanda KowalczykMaria Chikina

❮ Previous
Next ❯

Software Mentioned

TRIMAL
ANCORA
BLASTN
APE
UCNEbase
MAFFT
mVISTA
Ensembl genome browser
MEGABLAST
DC

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Genome Research
Dan Choffnes InadaMichael Freeling
Clinical Nurse Specialist CNS
P C Beecroft
Clinical Nurse Specialist CNS
P C Beecroft
© 2021 Meta ULC. All rights reserved