Sequence similarity

Ebook "Introduction to computational molecular biology" brings together major results in the field, in coherent and readable format. Setubal and Meidanis present a representative sample of problems in molecular biology, focusing on the algorithms that have been proposed to solve them. Readers will find background material on molecular biology, definitions of key terms, descriptions of models, and a full sample of algorithmic results.

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Inflammatory breast cancer (IBC) has a highly invasive and metastatic phenotype. However, little is known about its genetic drivers. To address this, we report the largest cohort of whole-genome sequencing (WGS) of IBC cases.

14p vibransone 28-03-2024 3 2   Download

The diagnostic rate of Mendelian disorders in sequencing studies continues to increase, along with the pace of novel disease gene discovery. However, variant interpretation in novel genes not currently associated with disease is particularly challenging and strategies combining gene functional evidence with approaches that evaluate the phenotypic similarities between patients and model organisms have proven successful.

20p viellison 28-03-2024 1 1   Download

Ebook "The BRICHOS domain: Its proproteins and functions" summarizes the current research on the novel BRICHOS domain, which is a chaperone domain found in a variety of proteins and is shown to exhibit anti-amyloidogenic chaperone-like functions. The BRICHOS domain is defined from sequence similarities, lacks established physiological function(s) and is found about 10 distantly related pro-protein families, several of which are associated with human disease.

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Previous studies have shown that Family with sequence similarity 134 member B (FAM134B) was involved in the occurrence and development of malignancy, however, the function and molecular mechanism of FAM134B in Hepatocellular Carcinoma (HCC) radiotherapy resistance remain unclear.

11p vioracle 29-09-2023 5 2   Download

Part 2 book "The improvement of technology transfer" includes content: Interviews with company representatives and university researchers, recommendations for actions, technology transfer in Styria - Qualitative similarities and differences compared to other studies; discussion and further need for research.

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The use of DNA barcodes is a molecular method commonly used for the identification of specimens that are difficult to pinpoint accurately by traditional morphological methods. DNA barcoding uses standard short genomic regions that are universally present in target lineages and has sufficient sequence variation to identify species in the genus.

9p vicaptainmarvel 21-04-2023 4 2   Download

Endophytic fungi, microfungi that internally infect living plant tissues, are reported to have the ability to synthesize many enzymes, plant growth hormones and pharmaceutically active compounds similar to those in their hosted plants. This has opened a potential path of using endophytic fungi as a bioreactor for mass production of bioactive compounds at a lower cost.

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A new species Pseudocercospora solanicola is discovered causing severe leaf spot disease on Solanum nigrum from Sonebhadra. Species is described and illustrated based on morphology, molecular sequence analysis and phylogeny of the large subunit (LSU) and internal transcribed spacer region of the nuclear ribosomal RNA (rRNA) gene. Morphologically, new species has similarity with allied species in Pseudocercospora but differs in having black circular, velvety leaf spot and size of stromata, conidia and conidiophores. A key to Pseudocercospora species on Solanum has been provided.

10p lyhuyenthu 31-01-2023 5 2   Download

Objective of the present study was to sequence chloroplast genomes of two cultivars of broccoli: Marathon and Green sprout. The sequencing was done by next generation sequencing. The analysis was performed using Velvet, Geneious, GeSeq, tRNAscan-SE, ARAGORN, OrganellarGenomeDRAW, IRscope and REPuter. The genomes of both cultivars showed highly similar quadripartite structure of 153,365 bp. The LSC (83,136 bp) and SSC (17,835 bp) regions were separated by a pair of IR (26,197 bp) region.

11p lyhuyenthu 31-01-2023 2 2   Download

Here we release a new version of EchinoDB, EchinoDB v2.0 (https://echinodb.uncc.edu). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity.

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DNA barcoding is a short DNA fragment, is used to distinguish between species, especially morphologically similar species and processed specimens that are difficult to distinguish species. For plants, the regions of DNA used as barcodes in identification or taxonomy are usually sequences of the chloroplast genome and the nuclear genome, including the coding regions and the non-coding regions.

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In the study "Genetic relationship analysis of Dendrobium anosmum Lindl. var. semialba based on the chloroplast matK and rbcL genes", the genetic relationship of Dendrobium anosmum Lindl. var. semialba species was determined based on the analysis of chloroplast matK, rbcL gene sequences. The matK and rbcL genes of twelve species were amplified and their DNA sequenced.chloroplast matK and rbcL genes

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Despite rapid progress of next-generation sequencing (NGS) technologies, the disease-causing genes underpinning about half of all Mendelian diseases remain elusive. One main challenge is the high genetic heterogeneity of Mendelian diseases in which similar phenotypes are caused by different genes and each gene only accounts for a small proportion of the patients.

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Dashing is a fast and accurate software tool for estimating similarities of genomes or sequencing datasets. It uses the HyperLogLog sketch together with cardinality estimation methods that are specialized for set unions and intersections.

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Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number.

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As single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed, so have analysis methods. Many methods have been tested, developed, and validated using simulated datasets. Unfortunately, current simulations are often poorly documented, their similarity to real data is not demonstrated, or reproducible code is not available.

15p vialfrednobel 29-01-2022 11 0   Download

The utility of experiments in model organisms such as mice to provide insights into human health and disease depends on the similarity of the fundamental physiological, cellular, and molecular processes across species. A new study helps resolve a controversy about determinants of gene expression variability and might facilitate the effective translation of research results across species.

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It is a major challenge to integrate single-cell sequencing data across experiments, conditions, batches, time points, and other technical considerations. New computational methods are required that can integrate samples while simultaneously preserving biological information.

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To understand diversity in enormous collections of genome sequences, we need computationally scalable tools that can quickly contextualize individual genomes based on their similarities and identify features of each genome that make them unique.

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