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41.
Bart HJ van den Berg Jay H Konieczka Fiona M McCarthy Shane C Burgess 《BMC bioinformatics》2009,10(1):30
Background
Systems biology modeling from microarray data requires the most contemporary structural and functional array annotation. However, microarray annotations, especially for non-commercial, non-traditional biomedical model organisms, are often dated. In addition, most microarray analysis tools do not readily accept EST clone names, which are abundantly represented on arrays. Manual re-annotation of microarrays is impracticable and so we developed a computational re-annotation tool (ArrayIDer) to retrieve the most recent accession mapping files from public databases based on EST clone names or accessions and rapidly generate database accessions for entire microarrays. 相似文献42.
Richard A Notebaart Frank HJ van Enckevort Christof Francke Roland J Siezen Bas Teusink 《BMC bioinformatics》2006,7(1):296
Background
The genomic information of a species allows for the genome-scale reconstruction of its metabolic capacity. Such a metabolic reconstruction gives support to metabolic engineering, but also to integrative bioinformatics and visualization. Sequence-based automatic reconstructions require extensive manual curation, which can be very time-consuming. Therefore, we present a method to accelerate the time-consuming process of network reconstruction for a query species. The method exploits the availability of well-curated metabolic networks and uses high-resolution predictions of gene equivalency between species, allowing the transfer of gene-reaction associations from curated networks. 相似文献43.
A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes 总被引:1,自引:0,他引:1
John M Hickey Brian P Kinghorn Bruce Tier James F Wilson Neil Dunstan Julius HJ van der Werf 《遗传、选种与进化》2011,43(1):12
Background
Knowing the phase of marker genotype data can be useful in genome-wide association studies, because it makes it possible to use analysis frameworks that account for identity by descent or parent of origin of alleles and it can lead to a large increase in data quantities via genotype or sequence imputation. Long-range phasing and haplotype library imputation constitute a fast and accurate method to impute phase for SNP data.Methods
A long-range phasing and haplotype library imputation algorithm was developed. It combines information from surrogate parents and long haplotypes to resolve phase in a manner that is not dependent on the family structure of a dataset or on the presence of pedigree information.Results
The algorithm performed well in both simulated and real livestock and human datasets in terms of both phasing accuracy and computation efficiency. The percentage of alleles that could be phased in both simulated and real datasets of varying size generally exceeded 98% while the percentage of alleles incorrectly phased in simulated data was generally less than 0.5%. The accuracy of phasing was affected by dataset size, with lower accuracy for dataset sizes less than 1000, but was not affected by effective population size, family data structure, presence or absence of pedigree information, and SNP density. The method was computationally fast. In comparison to a commonly used statistical method (fastPHASE), the current method made about 8% less phasing mistakes and ran about 26 times faster for a small dataset. For larger datasets, the differences in computational time are expected to be even greater. A computer program implementing these methods has been made available.Conclusions
The algorithm and software developed in this study make feasible the routine phasing of high-density SNP chips in large datasets. 相似文献44.
KLARA BJÖRG JAKOBSDÓTTIR þÓRA DÖGG JÖRUNDSDÓTTIR SIGURLAUG SKÍRNISDÓTTIR SIGRÍÐUR HJÖRLEIFSDÓTTIR GUÐMUNDUR Ó. HREGGVIÐSSON ANNA KRISTÍN DANÍELSDÓTTIR CHRISTOPHE PAMPOULIE 《Molecular ecology resources》2006,6(2):337-339
Nine out of 22 microsatellite primers tested were successfully amplified on three samples of cod Gadus morhua L. (two contemporary and one archived otolith samples). All loci were polymorphic (5–23 alleles/locus). The average observed heterozygosity across loci and samples was 0.625, ranging from 0.294 to 0.895 at each locus. All loci were under Hardy–Weinberg equilibrium, except PGmo56 that showed significant excess of heterozygotes in all studied samples. The isolated loci were suitable for degraded DNA and therefore useful for conducting a long‐term temporal study with DNA obtained from archived otoliths of cod. 相似文献
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Linda May Anita HJ van den Biggelaar David van Bodegom Hans J Meij Anton JM de Craen Joseph Amankwa Marijke Frölich Maris Kuningas Rudi GJ Westendorp 《Immunity & ageing : I & A》2009,6(1):1-7
Hutchinson-Gilford progeria syndrome (HGPS) is a rare premature aging disorder that belongs to a group of conditions called laminopathies which affect nuclear lamins. Mutations in two genes, LMNA and ZMPSTE24, have been found in patients with HGPS. The p.G608G LMNA mutation is the most commonly reported mutation. The aim of this work was to compile a comprehensive literature review of the clinical features and genetic mutations and mechanisms of this syndrome as a contribution to health care workers. This review shows the necessity of a more detailed clinical identification of Hutchinson-Gilford progeria syndrome and the need for more studies on the pharmacologic and pharmacogenomic approach to this syndrome. 相似文献
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