X-Meeting presentations

TSSFINDER—FAST AND ACCURATE AB INITIO PREDICTION OF THE CORE PROMOTER IN EUKARYOTIC GENOMES

Published in 26/04/2022 - ISBN: 978-65-5941-645-5

Link All Papers
LinkSubmission
Paper Title
TSSFINDER—FAST AND ACCURATE AB INITIO PREDICTION OF THE CORE PROMOTER IN EUKARYOTIC GENOMES
Authors
  • Mauro de Medeiros Oliveira
  • Ígor Bonadio
  • Alicia Lie de Melo
  • Glaucia Souza Mendes
  • Alan Durham
Modality
Xpress presentation
Subject area
Database and Software Development
Publishing Date
26/04/2022
Country of Publishing
Brasil
Language of Publishing
Inglês
Paper Page
https://www.even3.com.br/anais/xmeetingxp2021/423084-tssfinderfast-and-accurate-ab-initio-prediction-of-the-core-promoter-in-eukaryotic-genomes
ISBN
978-65-5941-645-5
Keywords
transcription start site, promoter region, annotation of genomes, conditional random fields
Summary
Promoter annotation is an important task in the analysis of a genome. One of the main challenges for this task is locating the border between the promoter region and the transcribing region of the gene, the transcription start site (TSS). The TSS is the reference point to delimit the DNA sequence responsible for the assembly of the transcriptional complex. To delimit the promoter region, it is important to locate the closest TSS to the site of the beginning of the translation, as the same gene can have more than one TSS. Here we present TSSFinder, a new software for the prediction of the TSS signal of eukaryotic genes that is significantly more accurate than other available software. We currently are the only application to offer pre-trained models for six different eukaryotic organisms: Arabidopsis thaliana, Drosophila melanogaster, Gallus gallus, Homo sapiens, Oryza sativa and Saccharomyces cerevisiae. Additionally, our software can be easily customized for specific organisms using as few as 125 DNA sequences with a validated TSS signal and their corresponding genomic locations as a training set. We currently include in the prediction model only four types of information: putative TATA-box location, when available, distance from the TSS to the TATA-box, distance from the TSS to the start codon, and composition of the TSS region. TSSFinder’s speed and accuracy make this software a valuable new tool for the annotation of genomes. TSSFinder source code and docker container can be downloaded from http://tssfinder.github.io. Alternatively, TSSFinder is also available as a web service at http://sucest-fun.org/wsapp/tssfinder/. (This abstract is in reference to a previously published article, and it’s intended for promotion purposes only).
Title of the Event
X-Meeting XPerience 2021
Title of the Proceedings of the event
X-Meeting presentations
Name of the Publisher
Even3
Means of Dissemination
Meio Digital

How to cite

OLIVEIRA, Mauro de Medeiros et al.. TSSFINDER—FAST AND ACCURATE AB INITIO PREDICTION OF THE CORE PROMOTER IN EUKARYOTIC GENOMES.. In: X-Meeting presentations. Anais...São Paulo(SP) AB3C, 2021. Available in: https//www.even3.com.br/anais/xmeetingxp2021/423084-TSSFINDERFAST-AND-ACCURATE-AB-INITIO-PREDICTION-OF-THE-CORE-PROMOTER-IN-EUKARYOTIC-GENOMES. Access in: 18/06/2025

Paper

Even3 Publicacoes