FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting

FOOTER is a newly developed algorithm that analyzes homologous mammalian promoter sequences in order to identify transcriptional DNA regulatory ‘signals’. FOOTER uses prior knowledge about the binding site preferences of the transcription factors (TFs) in the form of position-specific scoring matric...

Descripción completa

Detalles Bibliográficos
Autores principales: Corcoran, David L., Feingold, Eleanor, Benos, Panayiotis V.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160181/
https://www.ncbi.nlm.nih.gov/pubmed/15980508
http://dx.doi.org/10.1093/nar/gki420
_version_ 1782124371021660160
author Corcoran, David L.
Feingold, Eleanor
Benos, Panayiotis V.
author_facet Corcoran, David L.
Feingold, Eleanor
Benos, Panayiotis V.
author_sort Corcoran, David L.
collection PubMed
description FOOTER is a newly developed algorithm that analyzes homologous mammalian promoter sequences in order to identify transcriptional DNA regulatory ‘signals’. FOOTER uses prior knowledge about the binding site preferences of the transcription factors (TFs) in the form of position-specific scoring matrices (PSSMs). The PSSM models are generated from known mammalian binding sites from the TRANSFAC database. In a test set of 72 confirmed binding sites (most of them not present in TRANSFAC) of 19 TFs, it exhibited 83% sensitivity and 72% specificity. FOOTER is accessible over the web at .
format Text
id pubmed-1160181
institution National Center for Biotechnology Information
language English
publishDate 2005
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-11601812005-06-29 FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting Corcoran, David L. Feingold, Eleanor Benos, Panayiotis V. Nucleic Acids Res Article FOOTER is a newly developed algorithm that analyzes homologous mammalian promoter sequences in order to identify transcriptional DNA regulatory ‘signals’. FOOTER uses prior knowledge about the binding site preferences of the transcription factors (TFs) in the form of position-specific scoring matrices (PSSMs). The PSSM models are generated from known mammalian binding sites from the TRANSFAC database. In a test set of 72 confirmed binding sites (most of them not present in TRANSFAC) of 19 TFs, it exhibited 83% sensitivity and 72% specificity. FOOTER is accessible over the web at . Oxford University Press 2005-07-01 2005-06-27 /pmc/articles/PMC1160181/ /pubmed/15980508 http://dx.doi.org/10.1093/nar/gki420 Text en © The Author 2005. Published by Oxford University Press. All rights reserved
spellingShingle Article
Corcoran, David L.
Feingold, Eleanor
Benos, Panayiotis V.
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
title FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
title_full FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
title_fullStr FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
title_full_unstemmed FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
title_short FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
title_sort footer: a web tool for finding mammalian dna regulatory regions using phylogenetic footprinting
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160181/
https://www.ncbi.nlm.nih.gov/pubmed/15980508
http://dx.doi.org/10.1093/nar/gki420
work_keys_str_mv AT corcorandavidl footerawebtoolforfindingmammaliandnaregulatoryregionsusingphylogeneticfootprinting
AT feingoldeleanor footerawebtoolforfindingmammaliandnaregulatoryregionsusingphylogeneticfootprinting
AT benospanayiotisv footerawebtoolforfindingmammaliandnaregulatoryregionsusingphylogeneticfootprinting

Ejemplares similares