Cargando…

COTRASIF: conservation-aided transcription-factor-binding site finder

COTRASIF is a web-based tool for the genome-wide search of evolutionary conserved regulatory regions (transcription factor-binding sites, TFBS) in eukaryotic gene promoters. Predictions are made using either a position-weight matrix search method, or a hidden Markov model search method, depending on...

Descripción completa

Detalles Bibliográficos
Autores principales:	Tokovenko, Bogdan, Golda, Rostyslav, Protas, Oleksiy, Obolenskaya, Maria, El'skaya, Anna
Formato:	Texto
Lenguaje:	English
Publicado:	Oxford University Press 2009
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2673430/ https://www.ncbi.nlm.nih.gov/pubmed/19264796 http://dx.doi.org/10.1093/nar/gkp084

Ejemplares similares

Disentangling transcription factor binding site complexity
por: Eggeling, Ralf
Publicado: (2018)

IC-Finder: inferring robustly the hierarchical organization of chromatin folding
por: Haddad, Noelle, et al.
Publicado: (2017)

Human Splicing Finder: an online bioinformatics tool to predict splicing signals
por: Desmet, François-Olivier, et al.
Publicado: (2009)

Evolutionary computation for discovery of composite transcription factor binding sites
por: Fogel, Gary B., et al.
Publicado: (2008)

exFINDER: identify external communication signals using single-cell transcriptomics data
por: He, Changhan, et al.
Publicado: (2023)

ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites
por: Lelieveld, Stefan H., et al.
Publicado: (2016)

Optimized detection of transcription factor-binding sites in ChIP-seq experiments
por: Elo, Laura L., et al.
Publicado: (2012)

Improved predictions of transcription factor binding sites using physicochemical features of DNA
por: Maienschein-Cline, Mark, et al.
Publicado: (2012)

A novel method for improved accuracy of transcription factor binding site prediction
por: Khamis, Abdullah M, et al.
Publicado: (2018)

Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli
por: Meysman, Pieter, et al.
Publicado: (2011)

Discovery and validation of information theory-based transcription factor and cofactor binding site motifs
por: Lu, Ruipeng, et al.
Publicado: (2017)

Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites
por: Jajamovich, Guido H., et al.
Publicado: (2011)

A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
por: Rye, Morten Beck, et al.
Publicado: (2011)

A flexible integrative approach based on random forest improves prediction of transcription factor binding sites
por: Hooghe, Bart, et al.
Publicado: (2012)

Direct optical mapping of transcription factor binding sites on field-stretched λ-DNA in nanofluidic devices
por: Sriram, K. K., et al.
Publicado: (2014)

TFforge utilizes large-scale binding site divergence to identify transcriptional regulators involved in phenotypic differences
por: Langer, Björn E, et al.
Publicado: (2019)

Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction
por: Salama, Rafik A., et al.
Publicado: (2010)

Detecting cis-regulatory binding sites for cooperatively binding proteins
por: van Oeffelen, Liesbeth, et al.
Publicado: (2008)

Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP
por: Ameur, Adam, et al.
Publicado: (2009)

Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices
por: Oh, Young Min, et al.
Publicado: (2012)

Nanobody®-based chromatin immunoprecipitation/micro-array analysis for genome-wide identification of transcription factor DNA binding sites
por: Nguyen-Duc, Trong, et al.
Publicado: (2013)

Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes
por: Kuang, Zheng, et al.
Publicado: (2018)

DBSI: DNA-binding site identifier
por: Zhu, Xiaolei, et al.
Publicado: (2013)

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis
por: Boeva, Valentina, et al.
Publicado: (2010)

TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information
por: Kulkarni, Shubhada R, et al.
Publicado: (2018)

Conservative site-specific and single-copy transgenesis in human LINE-1 elements
por: Vijaya Chandra, Shree Harsha, et al.
Publicado: (2016)

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life
por: Friedel, Caroline C., et al.
Publicado: (2009)

Identifying RNA-binding residues based on evolutionary conserved structural and energetic features
por: Chen, Yao Chi, et al.
Publicado: (2014)

Evolutionary coupling analysis identifies the impact of disease-associated variants at less-conserved sites
por: Kim, Donghyo, et al.
Publicado: (2019)

CLIP-based prediction of mammalian microRNA binding sites
por: Liu, Chaochun, et al.
Publicado: (2013)

Probing binding hot spots at protein–RNA recognition sites
por: Barik, Amita, et al.
Publicado: (2016)

Detection of RNA–DNA binding sites in long noncoding RNAs
por: Kuo, Chao-Chung, et al.
Publicado: (2019)

Varying levels of complexity in transcription factor binding motifs
por: Keilwagen, Jens, et al.
Publicado: (2015)

SEASTAR: systematic evaluation of alternative transcription start sites in RNA
por: Qin, Zhiyi, et al.
Publicado: (2018)

Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins
por: Zeng, Jue, et al.
Publicado: (2008)

MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
por: Moses, Alan M, et al.
Publicado: (2004)

From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data
por: Bottini, Silvia, et al.
Publicado: (2017)

Construction of mate pair full-length cDNAs libraries and characterization of transcriptional start sites and termination sites
por: Matsumoto, Kyoko, et al.
Publicado: (2014)

Isolation of a site-specifically modified RNA from an unmodified transcript
por: Hou, Ya-Ming, et al.
Publicado: (2006)

Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes
por: Zhang, Shaoqiang, et al.
Publicado: (2009)

Cannot write session to /tmp/vufind_sessions/sess_sn3s5up4fnuus1o9k72dqb6apj