The Lagan Toolkit is a software package for comparison of genomic sequences. It includes the CHAOS local alignment program, LAGAN global alignment program for two, or more sequences and Shuffle-LAGAN, a “glocal” ali...
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The Lagan Toolkit is a software package for comparison of genomic sequences. It includes the CHAOS local alignment program, LAGAN global alignment program for two, or more sequences and Shuffle-LAGAN, a “glocal” alignment method that handles genomic rearrangements in a global alignment framework. The alignment programs included in the Lagan Toolkit have been widely used to compare genomes of many organisms, from bacteria to large mammalian genomes. This chapter provides an overview of the algorithms used by the LAGAN programs to construct genomic alignments, explains how to build alignments using either the standalone program or the web server, and discusses some of the common pitfalls users encounter when using the toolkit. less
The comparison of genomic sequences plays a key role in determining the structural and functional relationships between genes. This comparison is carried out by identifying the similarities, differences and mutations ...
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The comparison of genomic sequences plays a key role in determining the structural and functional relationships between genes. This comparison is carried out by identifying the similarities, differences and mutations between genomic sequences. This makes it possible to study and analyze the genetic and the evolutionary relationships between organisms. alignment algorithms have been in the spotlight for the last few decades, due to a vast genomic data explosion. They have attracted a great deal of interest from many researchers who focus on the development of practical solutions to ensure effective alignments with an optimal response time. In this paper, a novel algorithm based on Discrete To Continuous "DTC" approach has been developed. The proposed methodology was compared against other existing methods, which are largely based on the concept of string matching. Experimental results show that the DTC algorithm delivers supremely efficient alignment with a reduced response time.
Disorders of the cardiovascular system are often caused by the interaction of genetic and environmental factors that jointly contribute to individual susceptibility. Genomic data and bioinformatics tools generated fro...
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Disorders of the cardiovascular system are often caused by the interaction of genetic and environmental factors that jointly contribute to individual susceptibility. Genomic data and bioinformatics tools generated from genome projects, coupled with functional verification, offer novel approaches to study both rare single-gene and complex multigenic cardiovascular diseases. These approaches include gene mapping using genome variation, especially single-nucleotide polymorphisms and comparative genomics within and between species. This chapter illustrates the major genome resources, associated bioinformatics tools, and their potential application in cardiovascular research. less
Comprehensive two-dimensional gas chromatography – time-of-flight mass spectrometry (GC × GC–TOF-MS) is applied to the comparative metabolic fingerprinting of physiological fluids. Stable isotope-labeled intern...
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Comprehensive two-dimensional gas chromatography – time-of-flight mass spectrometry (GC × GC–TOF-MS) is applied to the comparative metabolic fingerprinting of physiological fluids. Stable isotope-labeled internal standards plus norvaline serve as extraction standards and are added to the blanks, controls and patient samples prior to protein precipitation with methanol. The extracts are evaporated to complete dryness and derivatized in two steps using methoximation with methoxylamine hydrochloride (MeOx) and silylation with N-methyl-N-trimethylsily- trifluoroacetamide (MSTFA). Between derivatization steps a second internal standard containing odd-numbered, saturated straight chain fatty acids is added for quality control and to normalize retention time shifts. After GC × GC–TOF-MS analysis raw data are processed, aligned, and combined in one data matrix for subsequent statistical evaluation. Both a custom-made and the NIST 05 library are used to preliminarily identify significant metabolites. For verification purposes, commercial standards are run individually. Absolute quantification of selected metabolites is achieved by using a multi-point calibration curve and isotope-labeled internal standards. less
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