14 papers · ranked by Valyu relevance
Geo Pertea, Mihaela Pertea
Summary: GTF (Gene Transfer Format) and GFF (General Feature Format) are popular file formats used by bioinformatics programs to represent and exchange information about various genomic features, such as gene and transcript locations and structure. GffRead and GffCompare are open source programs that provide extensive…
Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan + 1 more
'Thomas Shafee'] Transcriptomics technologies are the techniques used to study an organism’s [transcriptome](), the sum of all of its [RNA transcripts](). The information content of an organism is recorded in the DNA of its [genome]() and [expressed]() through [transcription](). Here, [mRNA]() serves as a transient…
Houjun Liu, Brian MacWhinney, Davida Fromm, Alyssa Lanzi
Purpose: A major barrier to the wider use of language sample analysis (LSA) is the fact that transcription is very time intensive. Methods that can reduce the required time and effort could help in promoting the use of LSA for clinical practice and research. Method: This article describes an automated pipeline, called…
Wend Yam D D Ouedraogo, Aida Ouangraoua
Eukaryotic genes can encode multiple distinct transcripts through the alternative splicing (AS) of genes. Interest in the AS mechanism and its evolution across different species has stimulated numerous studies, leading to several databases that provide information on AS and transcriptome data across multiple eukaryotic…
Timothy R. Fallon, Tereza Čalounová, Martin Mokrejš, Jing-Ke Weng + 1 more
'Tomáš Pluskal'] Background RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The complexity of these de novo transcriptomics workflows therefore…
Joe Nockels, Paul Gooding, Sarah Ames, Melissa Terras
Handwritten Text Recognition (HTR) technology is now a mature machine learning tool, becoming integrated in the digitisation processes of libraries and archives, speeding up the transcription of primary sources and facilitating full text searching and analysis of historic texts at scale. However, research into how HTR…
Tiffany Leung, Jing Wang, Seongsoon Kim, Michael Burns + 14 more
'Yang Liu' 'Thomas Soroski' 'Thiago da Cunha Vasco' 'Sally Newton-Mason' 'Saffrin Granby' 'Caitlin Lewis' 'Anuj Harisinghani' 'Matteo Rizzo' 'Cristina Conati' 'Gabriel Murray' 'Giuseppe Carenini' 'Thalia S Field' 'Hyeju Jang'] Background Speech data for medical research can be collected noninvasively and in large…
Mariia Zelenskaia, Yazhini Arangasamy, Milot Mirdita, Johannes Söding + 2 more
Transcriptome annotation is the task of associating biological and functional context to RNA-Seq data. This represents an essential step in rendering the data usable, especially in cases when a reference genome is absent (). The process typically uses protein sequences, translated in silico from pre-assembled…
Karmel A. Allison, Minna U. Kaikkonen, Terry Gaasterland, Christopher K. Glass
'Christopher K. Glass'] Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput sequencing methods that enables new insights into transcriptional dynamics within a cell. However, GRO-sequencing presents new algorithmic challenges, as existing analysis platforms for ChIP-seq and RNA-seq…
Joanna Moreton, Abril Izquierdo, Richard D. Emes
De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome.…
Yan O Zubo, Victor V Kusnetsov, Thomas Börner, Karsten Liere
Transcriptional activity of entire genes in chloroplasts is usually assayed by run-on analyses. To determine not only the overall intensity of transcription of a gene, but also the rate of transcription from a particular promoter, we created the Reverse RNase Protection Assay (RePro): in-organello run-on transcription…
Jonathan S. Abebe, Yasmine Alwie, Erik Fuhrmann, Jonas Leins + 6 more
'Julia Mai' 'Ruth Verstraten' 'Sabrina Schreiner' 'Angus C. Wilson' 'Daniel P. Depledge' 'Evelien M. Adriaenssens'] Title: ABSTRACT Nanopore direct RNA sequencing (DRS) enables the capture and full-length sequencing of native RNAs, without recoding or amplification bias. Resulting data sets may be interrogated to…
Mary O. Richardson, Sean R. Eddy
Background In canonical protein translation, ribosomes initiate translation at a specific start codon, maintain a single reading frame throughout elongation, and terminate at the first in-frame stop codon. However, ribosomal behavior can deviate at each of these steps, sometimes in a programmed manner. Certain mRNAs…
Michael A. DeJesus, Chaitra Ambadipudi, Richard Baker, Christopher Sassetti + 2 more
'Christopher Sassetti' 'Thomas R. Ioerger' 'Paul P Gardner'] TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for…