MOTIVATION: Overlapping gene coding sequences (CDSs) are particularly common in viruses but also occur in more complex genomes. Detecting such genes with conventional gene-finding algorithms can be difficult for several reasons. If an overlapping CDS is on the same read-strand as a known CDS, ...
Diversifying regulatory sequences and using native microalgal coding sequences (CDSs) with higher GC content improved transgene expression and resulted in a remarkable trans-generational stability via reduced accumulation of sRNAs and DNA methylation. Further experiments in maize with transgenes individually...
are short and contribute to regulating the translation of the longer coding sequences (CDSs) located downstream.94,95,96,97,98 With this mindboggling complexity in mind, in this review we aim to provide an overview of cases in which the categorization of “coding gene” vs “non-coding gene...
Proteogenomics and ribosome profiling concurrently show that genes may code for both a large and one or more small proteins translated from annotated coding sequences (CDSs) and unannotated alternative open reading frames (named alternative ORFs or altORFs), respectively, but the stoichiometry between...
The origin of the proteoforms is clear from the structure of the FASTA headers: redundant sequences are reduced to a single entry with one main ID, and all other IDs are kept in the description line, between square brackets. The UniProt ID is preferentially selected as the main ID, and ...
each positioniover all proteins of sufficient length (so a different number of sequences may be averaged at each position). Note that while the native LFE of different CDSs within each genome varies considerably, the LFE of each native CDS is compared toits ownset of randomized sequences. ...
The number of predicted coding sequences (CDSs) correlates with genome size while the number of tRNA coding genes does not (Table 1). This is also apparent by comparing the number of tRNA genes in the SGM MtbH37Rv (4.4 Mbp; [29]) and RGM MsmegMC2-155 (7 Mbp; [30]), which carry...
Using this method, lncRNAs binding to ribosomes can also be analyzed. RNC-seq sequences the full-length RNA in translation, and the long-read length can effectively exclude the interference of small fragments of RNA and degraded RNA. Longer reads of RNC-seq can provide more information, make...
Transposable element (TE) sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes. Analysis of complete genome sequences have turned up numerous cases where TE sequences...
and where noN. meningitidishomologue is present to identify these CDSs (TR23 & TR25), the sequences of theN. gonorrhoeaeCDSs referred to are provided as additional material [seeAdditional file]. TheN. meningitidisserogroup C strain FAM18 genome sequence was obtained from the Wellcome Trust Sange...