DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes

Sebestyén, Endre; Nagy, Tibor; Suhai, Sándor; Barta, Endre

doi:10.1186/1471-2105-10-s6-s6

Cited by 7 publications

(6 citation statements)

References 26 publications

(35 reference statements)

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“…However, we still observed a bias in the number of applications exclusively implemented towards the characterization of promoter sequences (e.g. TFMExplorer [65], DoOPSearch [66], COTRASIF [67], Mapper [69], CoreTF [70], and Pscan [71], see Table 4). For this reason, tools such as CBS or GenomeSurveyor [68], which allow users to conduct virtual screenings on the full sequence of genomes, are much more informative.…”

Section: Resultsmentioning

confidence: 99%

CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes

Corominas

2012

BMC Genomics

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BackgroundInformation about the composition of regulatory regions is of great value for designing experiments to functionally characterize gene expression. The multiplicity of available applications to predict transcription factor binding sites in a particular locus contrasts with the substantial computational expertise that is demanded to manipulate them, which may constitute a potential barrier for the experimental community.ResultsCBS (Conserved regulatory Binding Sites, http://compfly.bio.ub.es/CBS) is a public platform of evolutionarily conserved binding sites and enhancers predicted in multiple Drosophila genomes that is furnished with published chromatin signatures associated to transcriptionally active regions and other experimental sources of information. The rapid access to this novel body of knowledge through a user-friendly web interface enables non-expert users to identify the binding sequences available for any particular gene, transcription factor, or genome region.ConclusionsThe CBS platform is a powerful resource that provides tools for data mining individual sequences and groups of co-expressed genes with epigenomics information to conduct regulatory screenings in Drosophila.

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Section: Resultsmentioning

confidence: 99%

CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes

Corominas

2012

BMC Genomics

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“…Other example of new tools are represented by the work of Sperber et al [ 65 ], who created 'RetroTector' for the study of retroviral elements in vertebrates; by the work of Rubino and Attimonelli [ 66 ], who present a new algorithm for the classification of sequences based on regular expression syntax; and by the work of Sebestyén et al [ 67 ] presenting DoOPSearch, a web-based tool using the comparative analysis of a large number of orthologous promoter regions to find common conserved motifs in the promoter regions of different chordate and plants genes, and to identify the overrepresented Gene Ontology terms for functional gene correlations.…”

Section: An Overview Of Proceeding Contentsmentioning

confidence: 99%

The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community

D’Elia¹,

Gisel²,

Eriksson

et al. 2009

BMC Bioinformatics

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The EMBnet Conference 2008, focusing on 'Leading Applications and Technologies in Bioinformatics', was organized by the European Molecular Biology network (EMBnet) to celebrate its 20 th anniversary. Since its foundation in 1988, EMBnet has been working to promote collaborative development of bioinformatics services and tools to serve the European community of molecular biology laboratories. This conference was the first meeting organized by the network that was open to the international scientific community outside EMBnet. The conference covered a broad range of research topics in bioinformatics with a main focus on new achievements and trends in emerging technologies supporting genomics, transcriptomics and proteomics analyses such as high-throughput sequencing and data managing, text and data-mining, ontologies and Grid technologies. Papers selected for publication, in this supplement to BMC Bioinformatics, cover a broad range of the topics treated, providing also an overview of the main bioinformatics research fields that the EMBnet community is involved in. EMBnet history, mission and activitiesEMBnet was established in 1988 as an initiative of the European Molecular Biology Laboratory (EMBL) [1]. At that time, high-speed data communication across Europe as well as bioinformatics were in their infancy. The EMBL was accumulating an ever-growing quantity of sequence data and both the molecular biology and the biotechnology research communities needed to have an easy and fast access to those data. Accessing a remote computer using an ordinary command-line oriented terminal was not enough. The solution for eliminating communication delays could only be found in a distribution of data and

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“…Most of these approaches used PWMs from the TRANSFAC database Matys et al (2006) and JASPAR Sandelin et al (2004). Moreover, a special database was created for the common conserved motifs in the plant and chordate genomes and then a tool called DoOpSearch was developed to find putative TFBSs Sebestyén et al (2009). The most recent work that used phylogenetic information to locate TFBS is ConTra v2 Broos et al (2011) which allows users to search for putative TFBSs in any genomic region (promoters,5-UTR,3-UTR or introns) for nine reference organisms.…”

Section: Introductionmentioning

confidence: 99%

ANFIS-based fuzzy systems for searching dna-protein binding sites

Wang

Alhamdoosh

Pedrycz

2016

Preprint

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Transcriptional regulation mainly controls how genes are expressed and how cells behave based on the transcription factor (TF) proteins that bind upstream of the transcription start sites (TSSs) of genes. These TF DNA binding sites (TFBSs) are usually short (5-15 base pairs) and degenerate (some positions can have multiple possible alternatives). Traditionally, computational methods scan DNA sequences using the position weight matrix (PWM) of a given TF, calculate binding scores for each K-mer against the PWM, and finally classify a K-mer as to whether it is a putative TFBS or a background sequence based on a cut-off threshold. The FSCAN system, which is proposed in this paper, employs machine learning techniques to build a learner model that is able to identify TFBSs in a set of bound sequences without the need for a cut-off threshold. Our proposed method utilizes fuzzy inference techniques along with a distribution-based filtering algorithm to predict the binding sites of a TF given its PWM model and phastCons scores for the input DNA sequences. Data imbalance reduction techniques are also used to ease the learning of the adaptive-neuro fuzzy inference system (ANFIS) algorithm. The proposed system is tested on 22 ChIP-chip sequence-sets from the Saccharomyces Cerevisiae genome. Our results show that FSCAN outperforms other approaches like MatInspector and MATCH and is quite robust. As more transcriptional data becomes available, our proposed framework encourages the use of fuzzy logic techniques in the prediction of TFBSs.

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DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes

Cited by 7 publications

References 26 publications

CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes

CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes

The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community

ANFIS-based fuzzy systems for searching dna-protein binding sites

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