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MEGA5: Molecular evolutionary genetics analysis using maximum . . .
, 2011
"... Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version ..."
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Cited by 7284 (25 self)
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Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version
Hidden Markov models for sequence analysis: extension and analysis of the basic method
, 1996
"... Hidden Markov models (HMMs) are a highly effective means of modeling a family of unaligned sequences or a common motif within a set of unaligned sequences. The trained HMM can then be used for discrimination or multiple alignment. The basic mathematical description of an HMM and its expectation-maxi ..."
Abstract
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Cited by 219 (23 self)
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strategies. Finally it is demonstrated on the SH2 domain how a domain can be found from unaligned sequences using a special model type. The experimental work was completed with the aid of the Sequence Alignment and Modeling software suite. 1 Introduction Since their introduction to the computational biology
A rticle DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution
"... Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories: 1) sequence retrieval, editing, manipulation, and conversion among more than 20 ..."
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Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories: 1) sequence retrieval, editing, manipulation, and conversion among more than 20
Simple Software for Microarray Image Analysis
"... A set of microarray images were acquired by a sequence of biological experiments which were scanned via a high resolution scanner. For each spot corresponding to a gene, the ratio of Cy3 and Cy5 fluorescent signal intensities was obtained and which may be normalied based on piecewise linear regressi ..."
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Cited by 1 (0 self)
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), N2 = 21 patients of hepatitis C virus (HCV), 1 patient clinically diagnosed to be infected with HCV as well as HBV, and 4 patients were neither HCV nor HBV infected. Simple software was developed to solve the following problems: (i) Detect differentially expressed genes and (ii) Select a subset
Impact of release intervals on empirical research into software evolution, with application to the maintainability of Linux
"... Abstract: In most empirical research on software evolution, analysis of the data is performed with respect to the release sequence number, rather than the release date. This distinction is important when the intervals between release dates vary widely, as is generally the case with open-source softw ..."
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Cited by 3 (0 self)
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Abstract: In most empirical research on software evolution, analysis of the data is performed with respect to the release sequence number, rather than the release date. This distinction is important when the intervals between release dates vary widely, as is generally the case with open
A Software Package for Managing and Evaluating DNA Sequence and Microsatellite Data
"... Abstract: We have surveyed three molecular biology labs in Germany and Vietnam to evaluate practical problems in the management of molecular genetics data. These labs are generating a large amount of heterogeneous genetic data. Without a long-term and uniform storage as well as the assistance of pr ..."
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Information Management System (LIMS). The system can be used to manage and evaluate DNA sequence and microsatellite data in both plant and animal breeding for all different species. Under Open Source GNU public license, our software package will be released via the virtualization technology.
BIGDATA: Small: DA: DCM: . . . for Biological Sequencing Data
, 2012
"... We will soon be able to exhaustively sequence the DNA and RNA of entire communities of bacteria, as well as every individual cell of a tumor. Both of these very different applications of sequencing share in the need to rapidly and efficiently sort through large amounts of noisy sequence data (dozens ..."
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: the relatively high error rate of 0.1-1%, per base, and the volume of data we can now easily acquire with sequencers such as Illumina HiSeq. For years, sequencing capacity has been doubling every 6 months – significantly faster than compute capacity. Since almost all extant bioinformatic analysis approaches
Public Databases and Software for the Pathway Analysis of Cancer Genomes
"... Abstract: The study of pathway disruption is key to understanding cancer biology. Advances in high throughput technologies have led to the rapid accumulation of genomic data. The explosion in available data has generated opportunities for inves-tigation of concerted changes that disrupt biological f ..."
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of genetic and epigenetic alterations. Genetic events such as chromosomal rearrangements, changes in gene dosage, and sequence mutations can infl uence gene expression patterns, which contribute to the hallmark phenotypes of cancer1,2. The inter-action between pathways and the involvement of pathways
SOFTWARE Open Access
"... Sequencing data analysis to a new level of automation Prerana Wagle1, Miloš Nikolić1,2 and Peter Frommolt1* Background: Next-Generation Sequencing (NGS) has emerged as a widely used tool in molecular biology. While time and cost for the sequencing itself are decreasing, the analysis of the massive a ..."
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Sequencing data analysis to a new level of automation Prerana Wagle1, Miloš Nikolić1,2 and Peter Frommolt1* Background: Next-Generation Sequencing (NGS) has emerged as a widely used tool in molecular biology. While time and cost for the sequencing itself are decreasing, the analysis of the massive
SOFTWARE Open Access
"... Background: Genomic islands play an important role in medical, methylation and biological studies. To explore the region, we propose a CpG islands prediction analysis platform for genome sequence exploration (CpGPAP). Results: CpGPAP is a web-based application that provides a user-friendly interface ..."
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Background: Genomic islands play an important role in medical, methylation and biological studies. To explore the region, we propose a CpG islands prediction analysis platform for genome sequence exploration (CpGPAP). Results: CpGPAP is a web-based application that provides a user
Results 1 - 10
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245
