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Genomic selection (GS) is a marker-assisted selection approach to enhance quantitative traits in breeding population in which whole genome single-nucleotide polymorphisms (SNPs) markers can be used to predict breeding values (BV). GS has been proved to increase breeding efficiency in both plant and animal breeding, such as dairy cattle, pig, rice, soybean and loblolly pine. Here, we propose a deep-learning...
With the rapid development of high-throughput sequencing technology, biomedical research has entered into the era of big data. It causes problems about storage and analysis of massive biological data which need to be solved by high-performance computing. Therefore, we build the localized high-performance one-stop data analysis platform to provide convenient and efficient computational analysis services...
Many genome-scale data are available in soybean including genomic sequence, transcriptomics (microarray, RNA-seq), proteomics and metabolomics datasets, together with growing knowledge of soybean in gene, microRNAs, pathways, and phenotypes. This represents rich and resourceful information which can provide valuable insights, if mined in an innovative and integrative manner and thus, the need for...
In this paper we proposed a new distance computing method for DNA sequences. Given a set of species, the method first codes the DNA sequences of each species into a characteristic vector, and then computes a distance matrix for the set of species based on these characteristic vectors. The distance matrix obtained can be used to construct phylogenetic trees for phylogenetic analysis. Such a method...
Detection of genomic DNA copy number variations (CNVs) can provide a complete and more comprehensive view of human disease. In this paper, we incorporate DNA copy number variation data derived from SNP arrays into a computational shrunken model and formalize the detection of copy number variations as a case-control classification problem. By shrinkage, the number of relevant CNVs to disease can be...
Analysis about EST data usually starts with EST clustering, the process of grouping fragments according their original consensus long sequence. The similarity between ESTs always means that part of the sequences match with each other in some way. Accurate clustering is quadratic in time in average EST length and numbers, and the number of ESTs in public EST database is increasing exponentially. With...
Infectious microorganisms represent the causes of many of the most common and dangerous diseases in our modern society. Two major problems exist when tackling the problem of infections: detection and treatment. Here we utilize two distinct nanotechnology platforms to combat these problems. First, we demonstrate a novel detection method for identifying Mycobacterium tuberculosis DNA using rolling circle...
In this study, the RAPD (Random Amplified Polymorphic DNA) technology was used to identify the genotypic variation between the parental strain and the shuffled strain of Streptomyces gilvosporeus. Firstly, RAPD conditions were optimized by orthogonal test. The results were as follows: DNA 60-150 ng, Taq DNA polymerase 1.0-1.5U, primer concentration 0.3-0.4 mmol/L, dNTPs concentration 200-250 μmol/L,...
CYP17 (17α-hydroxylase/17, 20-lyase) has been viewed as a critical enzyme for the biosynthesis of gonadal and adrenal steroids in vertebrates. According to a reported CYP17 gene of Strongylocentrotus purpuratus gene from NCBI, three pairs of primers were designed to clone CYP17 gene of Strongylocentrotus nudus,using RT-PCR. Three fragments were assembled into on contig of 1569bp, including full CDS...
Electric mechanical or chemical signals of biological origin delivered by human bodies can always be of interest for diagnosis, patient monitoring, and biomedical research. Such biomedical signals, namely biosignals, are usually presented by flat file format or proprietary format when digitized for acquisition, storage, transfer and analysis. Recent advances in the ubiquitous computing technology...
Consensus RNA secondary structure and helices are always required from several homologous sequences as the development of non-coding RNA. The problem can be solved by comparative sequence analysis methods, in which nearly all the algorithms are based on multiple sequence alignment. However, there are no effective models combining similarity and secondary structure. So far multiple sequence alignment...
The genome-wide disease association is a major interest of current genomics research. However, these works are limited by the high cost of genotyping large number of single nucleotide polymorphisms (SNPs). Therefore, it is essential to choose a small subset of informative SNPs (tagSNPs) to represent the rest of the SNPs. To find the minimum set of tagSNPs, we propose a new method that combines the...
Multiple-instance learning is a special machine learning algorithm between supervised learning and unsupervised learning, which has been used in medicine design, image retrieval and other research fields, and attained good performance. Diverse Density (DD) algorithm is a typical multiple- instance learning method. Due to the character of sparse positive instances, when classifying the bags which include...
Biology sequence database search is an important problem for bioinformatics research. The main search software BLAST is based on the BYP algorithm. In BYP, if the length of hit region is set long, it may lose similar appearance. Otherwise, there may be too many r-length regions from Aho-Corasik algorithm. Checking where exists any approximate alignments for the DNA or RNA sequence always spends much...
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