The definition of open reading frame revisited
P Sieber, M Platzer, S Schuster - Trends in Genetics, 2018 - cell.com
The term open reading frame (ORF) is of central importance to gene finding. Surprisingly, at
least three definitions are in use. We discuss several molecular biological and bioinformatics …
least three definitions are in use. We discuss several molecular biological and bioinformatics …
Unraveling the hidden universe of small proteins in bacterial genomes
S Miravet‐Verde, T Ferrar… - Molecular systems …, 2019 - embopress.org
Identification of small open reading frames (sm ORF s) encoding small proteins (≤ 100
amino acids; SEP s) is a challenge in the fields of genome annotation and protein discovery …
amino acids; SEP s) is a challenge in the fields of genome annotation and protein discovery …
ORFik: a comprehensive R toolkit for the analysis of translation
Background With the rapid growth in the use of high-throughput methods for characterizing
translation and the continued expansion of multi-omics, there is a need for back-end …
translation and the continued expansion of multi-omics, there is a need for back-end …
Are antisense proteins in prokaryotes functional?
Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes.
Across bacterial species hundreds of short open reading frames antisense to annotated …
Across bacterial species hundreds of short open reading frames antisense to annotated …
ProsmORF-pred: a machine learning-based method for the identification of small ORFs in prokaryotic genomes
Small open reading frames (smORFs) encoding proteins less than 100 amino acids (aa) are
known to be important regulators of key cellular processes. However, their computational …
known to be important regulators of key cellular processes. However, their computational …
Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting
L Fellner, S Simon, C Scherling, M Witting… - BMC evolutionary …, 2015 - Springer
Background Gene duplication is believed to be the classical way to form novel genes, but
overprinting may be an important alternative. Overprinting allows entirely novel proteins to …
overprinting may be an important alternative. Overprinting allows entirely novel proteins to …
Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection
The existence of overlapping genes (OLGs) with significant coding overlaps revolutionizes
our understanding of genomic complexity. We report two exceptionally long (957 nt and …
our understanding of genomic complexity. We report two exceptionally long (957 nt and …
Statistical analysis of synonymous and stop codons in pseudo-random and real sequences as a function of GC content
Abstract Knowledge of the frequencies of synonymous triplets in protein-coding and non-
coding DNA stretches can be used in gene finding. These frequencies depend on the GC …
coding DNA stretches can be used in gene finding. These frequencies depend on the GC …
Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales
S Siddaramappa, V Viswanathan… - Microbial …, 2018 - microbiologyresearch.org
The order Sphingomonadales is a taxon of bacteria with a variety of physiological features
and carotenoid pigments. Some of the coloured strains within this order are known to be …
and carotenoid pigments. Some of the coloured strains within this order are known to be …
Phenotype of htgA (mbiA), a recently evolved orphan gene of Escherichia coli and Shigella, completely overlapping in antisense to yaaW
L Fellner, N Bechtel, MA Witting, S Simon… - FEMS microbiology …, 2014 - academic.oup.com
Overlapping embedded genes, such as htgA/yaaW, are assumed to be rare in prokaryotes.
In Escherichia coli O157: H7, gfp fusions of both promoter regions revealed activity and …
In Escherichia coli O157: H7, gfp fusions of both promoter regions revealed activity and …