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Bioinformatics analysis

Tìm thấy 17+ kết quả cho từ khóa "Bioinformatics analysis"

Identification of key genes and pathways associated with feed efficiency of native chickens based on transcriptome data via bioinformatics analysis

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Identification of key genes and pathways associated with feed efficiency of native chickens based on transcriptome data via bioinformatics analysis. Background: Improving feed efficiency is one of the important breeding targets for poultry industry. The aim of current study was to investigate the breast muscle transcriptome data of native chickens divergent for feed efficiency.

Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides

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KB and SG performed bioinformatics analysis of the genomes. OR prepared functional annotations of the genomes.

Genome-wide miRNA analysis and integrated network for flavonoid biosynthesis in Osmanthus fragrans

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Via bioinformatics analysis, there are 47 conserved miRNA families and 88 novel miRNAs identified from flower and leaf samples.. The read numbers of the 47 conserved miRNA fam- ilies varied from 11 (miR5538) to miR166), which implies the expression patterns of different miRNA families dramatically differ.

Genome-wide identification of the class III POD gene family and their expression profiling in grapevine (Vitis vinifera L)

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The POD family members have been well-studied and characterized by bioinformatics analysis in several plant species, but no previous genome-wide analysis has been carried out of this gene family in grapevine to date.. Intriguingly, the integrated analysis of chromosomal mapping and gene collinearity analysis proposed that both dispersed and tandem duplication events contributed to the expansion of PODs in grapevine..

Transcriptomic analysis of sea cucumber (Holothuria leucospilota) coelomocytes revealed the echinoderm cytokine response during immune challenge

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In this study, high-throughput transcriptomic sequen- cing and bioinformatics analysis were performed on the primary coelomocytes isolated from the sea cucumber H. This study provides evidences for the potential roles of cytokines in the innate immunity of sea cucumber.. Primary coelomocytes isolated from the sea cucumber H..

Comprehensive analysis of the Gossypium hirsutum L. respiratory burst oxidase homolog (Ghrboh) gene family

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Zujun Yin of the Institute of Cotton Research, Chinese Academy of Agricultural Sciences, for providing valuable advice on bioinformatics analysis.. The funding agency played no role in the design of the study. in the collection, analyses, or interpretation of data. or in the writing of the manuscript, or in the decision to publish the result.. This article did not contain any studies with human participants or animals performed by any of the authors..

Genome-wide identification of the DUF668 gene family in cotton and expression profiling analysis of GhDUF668 in Gossypium hirsutum under adverse stress

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Identification and bioinformatics analysis of the cotton DUF668 gene. The number of amino acid residues, relative molecular mass, and theoret- ical isoelectric point of the GhDUF668 protein were calcu- lated by ExPASy software (http://cn.expasy.org/tools) [58].. Subcellular localization of the GhDUF668 protein was predicted by EuLoc online software (http://euloc.mbc.. Phylogeny and collinearity analysis of the cotton DUF668 gene family.

Transcriptome analysis uncovers the key pathways and candidate genes related to the treatment of Echinococcus granulosus protoscoleces with the repurposed drug pyronaridine

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RNA-seq bioinformatics analysis. The high-quality clean reads were aligned to the reference genome using the HIASAT (https://ccb.jhu.edu/software/hisat2/index.. nine downregulated genes: HSP72, ECSIT, SRF, SYF, LSM4, U2AF, and ABCB1) were selected from the top three enriched path- ways, and their gene expression levels in the control and PND-treated groups were evaluated. 3 Verification of the RNA-seq data by qRT-PCR. Bars represent the mean fold changes in the expression of eleven genes in E.

Identification and analysis of the FAD gene family in walnuts (Juglans regia L.) based on transcriptome data

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In this research, walnut kernels at dif- ferent stages of maturity were used as test materials to analyse the key gene family involved in unsaturated fatty acid synthesis based on bioinformatics analysis and transcriptome sequencing. This study explored the mechanism of walnut fatty acid formation, espe- cially the anabolic mechanism of unsaturated fatty acids, and the results provide a theoretical basis for the regulation of walnut fatty acid synthesis.

“Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

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This number has expanded rapidly in recent years, mainly due to the de- velopment of whole genome sequencing technologies as- sociated with the exponential increase in the number of bioinformatics analysis tools that produced massive amounts of information and increased the numbers of identified genes [25, 26]..

Genomewide analysis of circular RNA in pituitaries of normal and heat-stressed sows

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Then, we explored circRNA in the pituitary of heat- stressed and normal sows using RNA sequencing and bioinformatics analysis. Furthermore, the predicted circRNA – miRNA – mRNA interactions showed that some circRNAs might sponge miRNAs to regulate pituitary-specific genes and heat shock protein family members, indicating circRNA ’ s roles in pituitary hormone secretion and heat stress response..

Antimicrobial activity screening of rhizosphere soil bacteria from tomato and genome-based analysis of their antimicrobial biosynthetic potential

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In addition, from the large-scale bioinformatics analysis of the genomes from Bacillus genus, we found that NRPS and PKS-NRPS BGCs resources hidden in Bacillus species are frequently encoding highly con- served known compounds including surfactin, fengycin, bacillibactin, petrobactin, lichenysin and bacillaene.. (February 2017) from tomatoes grown in a garden in the village of Roden in the Netherlands and Almería in Spain, which were given to us by company Koppert and with their consent.

Integrated analysis of the responses of a circRNA-miRNA-mRNA ceRNA network to heat stress in rainbow trout (Oncorhynchus mykiss) liver

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In this study, the circRNA, miRNA and mRNA of rainbow trout under heat stress were mined by high-throughput sequen- cing and bioinformatics analysis. The identification and characterization of the regulatory mechanism of ceRNA is intended to provide improved recommenda- tions for relieving heat stress in rainbow trout.. Effects of heat stress on nonspecific immunity in rainbow trout. Overview of RNA-seq results in rainbow trout under heat stress.

Genome-wide analysis of Homo sapiens, Arabidopsis thaliana, and Saccharomyces cerevisiae reveals novel attributes of tailanchored membrane proteins

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Comprehensive bioinformatics analysis of the generated TAMP datasets revealed previously unappreciated common and species-specific features such as the unusual size distribution of and the propensity of TAMP proteins to be part of larger complexes.. Additionally, novel features of the amino acid sequences that anchor TAMPs to membranes were also revealed.. Full list of author information is available at the end of the article.

Identification of a quantitative trait loci (QTL) associated with ammonia tolerance in the Pacific white shrimp (Litopenaeus vannamei)

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DZ and CY wrote the manuscript and contributed in the bioinformatics analysis. XC, YL, HW, HL, and JL contributed in the bioinformatics analysis. Effect of ammonia on survival and adenylate energy charge in the shrimp Palaemonetes varians. Transcriptome analysis of the Hepatopancreas in the Pacific white shrimp (Litopenaeus vannamei) under acute Ammonia stress.

A study of the heterochronic sense/ antisense RNA representation in florets of sexual and apomictic Paspalum notatum

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MP: bioinformatics analysis, writing of the manuscript.

Hepatic transcriptome perturbations in dairy cows fed different forage resources

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Among the unique bio- logical pathways identified through bioinformatics analysis, glycan biosynthesis and metabolism and amino acid metab- olism were highly inhibited when the low-quality forage diet was fed. Co-expression net- work analysis indicated that the downregulated genes related to autophagy and translation played critical roles in the network. In addition, pyruvate metabolic process and other energy-requiring biological processes were enriched in the co-expression network.

Genome-wide analysis of MicroRNAmessenger RNA interactome in ex-vivo gill filaments, Anguilla japonica

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Bioinformatics analysis of the dysregulated miRs from the two time-points at high stringency of fil- tering (p <. 0.001) shortlisted two miR candidates, miR- 29b-3p and miR-200b-3p.

Genome-wide identification, characterization, and expression analysis of tea plant autophagy-related genes (CsARGs) demonstrates that they play diverse roles during development and under abiotic stress

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Bioinformatics analysis of CsARGs in tea plant. expasy.org/protparam. wolfpsort.org. To obtain the promoter sequences, the genome sequences of each CsARG gene were down- loaded from the two published tea plant genomes (‘Shu- ChaZao’ and ‘YunKang10’) in the TPIA database. The conserved domains of CsATG8s were identified using the MEME website (http://memesuite.org/) with optimum motifs.

Genome-wide analysis of the serine carboxypeptidase-like protein family in Triticum aestivum reveals TaSCPL184-6D is involved in abiotic stress response

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.. org/10.1093/bioinformatics/btx198.. https://doi.org/10.1093/nar/gks596.. org/10.1016/j.ijbiomac . https://doi.org/10.1093/nar/. https://doi.org/10.1104/pp.15.01667.. https://doi.org/10.1046/j.1365-313x x.. https://doi.org/10.1105/tpc