ArticleBriefings in bioinformatics2021
TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Multi-omic cell free DNA profiles of cerebral spinal fluid from lung cancer metastasis to the brain.NAR cancer · 2026Article
- Clusia genomes shed light on the evolution and diversity of crassulacean acid metabolism physiotypes.Nature communications · 2026Article
- A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest.Genome research · 2026Review
- Boosting Transcript Assembly via Delineating Transcript Start and End Sites.bioRxiv : the preprint server for biology · 2025Article
- Identification and application of bioparts for plant synthetic biology.Molecules and cells · 2025Review
- Nanopore-based cell-free DNA fragmentation and methylation profiles from the cerebral spinal fluid of patients with lung cancer brain metastases.bioRxiv : the preprint server for biology · 2025Article
- The gene regulatory mechanisms shaping the heterogeneity of venom production in the Cape coral snake.Genome biology · 2025Article
- Transposable Element Landscape in the Monotypic SpeciesBiomolecules · 2025Article
- Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.The Plant cell · 2024Article
- From qualitative to quantitative: the state of the art and challenges for plant synthetic biology.Quantitative biology (Beijing, China) · 2023Review
- Classification of Promoter Sequences from Human Genome.International journal of molecular sciences · 2023Article
- A mini-TGA protein modulates gene expression through heterogeneous association with transcription factors.Plant physiology · 2023Article
- Database of Potential Promoter Sequences in theBiology · 2022Article
- Sequence-based evaluation of promoter context for prediction of transcription start sites in Arabidopsis and rice.Scientific reports · 2022Article
- Supervised promoter recognition: a benchmark framework.BMC bioinformatics · 2022Article
- Genome-Wide Prediction of Transcription Start Sites in Conifers.International journal of molecular sciences · 2022Article
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Authors and funding
5 authors.
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Abstract
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 transcribing complex. As the same gene can have more than one TSS, so to delimit the promoter region, it is important to locate the closest TSS to the site of the beginning of the translation. This paper presents 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 only 125 DNA sequences with a validated TSS signal and corresponding genomic locations as a training set. TSSFinder is 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/.
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