Genome assembly databases are growing rapidly. The redundancy of sequence content between a new assembly and previous ones is neither conceptually nor algorithmically easy to measure. We introduce pertinent methods and DandD, a tool addressing how much new sequence is gained when a sequence collection grows. DandD can describe how much structural variation is discovered in each new human genome assembly and when discoveries will level off in the future. DandD uses a measure called δ ("delta"), developed initially for data compression and chiefly dependent on -mer counts. DandD rapidly estimates δ using genomic sketches. We propose δ as an alternative to --specific cardinalities when computing the Jaccard coefficient, thereby avoiding the pitfalls of a poor choice of . We demonstrate the utility of DandD's functions for estimating δ, characterizing the rate of pangenome growth, and computing all-pairs similarities using -independent Jaccard.
Background: Variants in have been reported to be associated with Leigh syndrome. However, further expansion of the -phenotype and variants spectrum of -related Leigh syndrome are still required.
Methods: Two patients diagnosed with Leigh syndrome were recruited, and whole-exome sequencing was performed to identify the genetic variants responsible for the abnormal gait, dystonia, and bilateral basal ganglia lesions, followed by validation using Sanger sequencing.
Background: Fat traits in cattle are considered important due to their contribution to beef eating quality and carcass economic value. Discovering the genes controlling fat traits in cattle will enable better selection of these traits, but identifying these genes in individual experiments has proven difficult. Compared to individual experiments, meta-analyses allow greater statistical power for detecting quantitative trait loci and identifying genes that influence single and multiple economically important fat traits.
tRNA-derived stress-induced RNAs (tiRNAs) are a new class of small non-coding RNA that have emerged as important regulators of cellular stress responses. tiRNAs are derived from specific tRNA cleavage by the stress-induced ribonuclease angiogenin (ANG). Loss-of-function mutations in the ANG gene are linked to amyotrophic lateral sclerosis (ALS), and elevated levels of specific tiRNAs were recently identified in ALS patient serum samples.
GIPhy - Genome Informatics and Phylogenetics, Biological Resource Center of Institut Pasteur, Institut Pasteur, Université de Paris, 75015, Paris, France.
A Gram-staining-positive, aerobic bacterium, designated strain JJ-181, was isolated from the root surface of soybean. Based on the 16S rRNA gene sequence similarities, strain JJ-181 was grouped into the genus Cohnella, most closely related to Cohnella hashimotonis F6_2S_P_1 (98.85%) and C.
Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, CEP 05508-090, São Paulo, SP, Brazil.
Tetrapedia diversipes is a Neotropical solitary bee commonly found in trap-nests, known for its morphological adaptations for floral oil collection and prepupal diapause during the cold and dry season. Here, we present the genome assembly of T. diversipes (332 Mbp), comprising 2,575 scaffolds, with 15,028 predicted protein-coding genes.
