A single-nucleotide polymorphism tagging set for human drug
... region in different people showing three bases where variation occurs. Each SNP has two possible alleles; the first SNP in panel a has the alleles C and T. ...
... region in different people showing three bases where variation occurs. Each SNP has two possible alleles; the first SNP in panel a has the alleles C and T. ...
Masters_Thesis_Final - JScholarship
... However, data from GWAS of over 240 traits and diseases, identifying over 3500 associated SNPs, shows that about 88% of these SNPs lie within non-coding region of the genome [5]. These non-coding variants are hypothesized to lie in regulatory regions of the genome, which regulate gene expression. So ...
... However, data from GWAS of over 240 traits and diseases, identifying over 3500 associated SNPs, shows that about 88% of these SNPs lie within non-coding region of the genome [5]. These non-coding variants are hypothesized to lie in regulatory regions of the genome, which regulate gene expression. So ...
High efficiency of site-directed mutagenesis mediated by a single
... Site-directed mutagenesis by unique restriction site elimination introduced by Deng and Nickoloff allows a site-specific mutagenesis of a plasmid DNA without any subcloning step (1). This procedure uses two mutagenic primers: one carries the desired mutation, the second, acting as a selection primer ...
... Site-directed mutagenesis by unique restriction site elimination introduced by Deng and Nickoloff allows a site-specific mutagenesis of a plasmid DNA without any subcloning step (1). This procedure uses two mutagenic primers: one carries the desired mutation, the second, acting as a selection primer ...
synthesis Gene Cluster of Streptomyces clavuligerus
... argR and argG (nt 4600 to 6604) corresponding to ORF5 and ORF6. The proteins encoded by ORF2, ORF3 and ORF4 were homologous with ArgJ, ArgB and ArgD of other organisms while ORF7 encodes argH. ORF8 was truncated and its deduced amino acid sequence does not correspond to any enzyme of the arginine bi ...
... argR and argG (nt 4600 to 6604) corresponding to ORF5 and ORF6. The proteins encoded by ORF2, ORF3 and ORF4 were homologous with ArgJ, ArgB and ArgD of other organisms while ORF7 encodes argH. ORF8 was truncated and its deduced amino acid sequence does not correspond to any enzyme of the arginine bi ...
S1 Appendix.
... database. (A) Header files contain genome coordinates, total number of features under analysis in the genome and structure of the other output files. (B) The Primer files show all forward and reverse primers for deleting or tagging ...
... database. (A) Header files contain genome coordinates, total number of features under analysis in the genome and structure of the other output files. (B) The Primer files show all forward and reverse primers for deleting or tagging ...
Ensembl Genome Browser - molecularevolution.org
... “Instant” refresh of selected set Flexible output to HTML table, FASTA, CSV, TSV, Excel … All Ensembl genes on chromosome 5 in GTF format, etc… ...
... “Instant” refresh of selected set Flexible output to HTML table, FASTA, CSV, TSV, Excel … All Ensembl genes on chromosome 5 in GTF format, etc… ...
2D Representation of Transcriptomes by t- SNE Exposes Relatedness between Human Tissues
... The use of dimensionality reduction methods such as multidimensional scaling (MDS) or principal component analysis (PCA) are popular techniques for data representation in low dimensions[1]. As an example, the use of MDS was used in a recent study from the GTEx consortium [1] where transcriptome data ...
... The use of dimensionality reduction methods such as multidimensional scaling (MDS) or principal component analysis (PCA) are popular techniques for data representation in low dimensions[1]. As an example, the use of MDS was used in a recent study from the GTEx consortium [1] where transcriptome data ...
The DNA sequence of human chromosome 21
... from pure gene predictions, and also anonymous complementary DNA sequences from those exhibiting similarities to known proteins or modular domains. The criteria governing the gene classi®cation were based on the results of the integrated results of computational analysis using exon prediction progra ...
... from pure gene predictions, and also anonymous complementary DNA sequences from those exhibiting similarities to known proteins or modular domains. The criteria governing the gene classi®cation were based on the results of the integrated results of computational analysis using exon prediction progra ...
1548 Tn Gene Is Borne by Composite Transposon Aminoglycoside
... resistant to amikacin, streptomycin-spectinomycin, sulfonamides, trimethoprim, neomycin, and chloramphenicol. By contrast, in the K802N recipient, the loss of resistance (i) to amikacin, streptomycin-spectinomycin, sulfonamides, and trimethoprim secondary to excision of Tn1548, (ii) to neomycin due ...
... resistant to amikacin, streptomycin-spectinomycin, sulfonamides, trimethoprim, neomycin, and chloramphenicol. By contrast, in the K802N recipient, the loss of resistance (i) to amikacin, streptomycin-spectinomycin, sulfonamides, and trimethoprim secondary to excision of Tn1548, (ii) to neomycin due ...
Naming `junk`: Human non-protein coding RNA (ncRNA) gene
... Previously, the majority of the human genome was thought to be ‘junk’ DNA with no functional purpose. Over the past decade, the field of RNA research has rapidly expanded, with a concomitant increase in the number of non-protein coding RNA (ncRNA) genes identified in this ‘junk’. Many of the encoded ...
... Previously, the majority of the human genome was thought to be ‘junk’ DNA with no functional purpose. Over the past decade, the field of RNA research has rapidly expanded, with a concomitant increase in the number of non-protein coding RNA (ncRNA) genes identified in this ‘junk’. Many of the encoded ...
Comparative Genomics of Microbes
... • Genome sequencing is just the beginning to appreciate biocomplexity • Sequence-based function assignment approaches fail as the sequence similarity drops … • Structure-based function prediction approaches are limited by the availability of structures, association of structural motifs & associated ...
... • Genome sequencing is just the beginning to appreciate biocomplexity • Sequence-based function assignment approaches fail as the sequence similarity drops … • Structure-based function prediction approaches are limited by the availability of structures, association of structural motifs & associated ...
A Novel Chimeric Low-Molecular-Weight Glutenin
... clustered in a separate group. With the LMW-GS gene group, three types of LMW-GS genes were divided into different subgroups but LMW-s- and LMW-m-type genes were shown to have higher homology. These results were consistent with their sequence characteristics and recent reports of An et al. (2006) an ...
... clustered in a separate group. With the LMW-GS gene group, three types of LMW-GS genes were divided into different subgroups but LMW-s- and LMW-m-type genes were shown to have higher homology. These results were consistent with their sequence characteristics and recent reports of An et al. (2006) an ...
Documentation - Broad Institute
... currently one of the best assemblers available to handle diverse viral genomes with 454 data. The Arachne assembler can be obtained at http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page. All the documentation on how to install and run the assembler can be found there. V-Profiler requ ...
... currently one of the best assemblers available to handle diverse viral genomes with 454 data. The Arachne assembler can be obtained at http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page. All the documentation on how to install and run the assembler can be found there. V-Profiler requ ...
Genome Biology and Evolution
... of U. diaspidicola has been sequenced from an insect that only has a single endosymbiont species (Sabree et al. 2012). Llaveia axin axin (Monophlebidae) harbors both endosymbionts previously found in scale insects: a flavobacterium and an enterobacterium (Rosenblueth et al. 2012). Llaveia axin axin ...
... of U. diaspidicola has been sequenced from an insect that only has a single endosymbiont species (Sabree et al. 2012). Llaveia axin axin (Monophlebidae) harbors both endosymbionts previously found in scale insects: a flavobacterium and an enterobacterium (Rosenblueth et al. 2012). Llaveia axin axin ...
Brandi Deptula Final Research Paper
... way to more efficient renewable energies, and may also aid in better processing of paper materials in mills. When searching for ways to breakdown and extract plant polysaccharides, it is reasonable to look at the microbial systems found in the guts of organisms such as termites that flourish on a di ...
... way to more efficient renewable energies, and may also aid in better processing of paper materials in mills. When searching for ways to breakdown and extract plant polysaccharides, it is reasonable to look at the microbial systems found in the guts of organisms such as termites that flourish on a di ...
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... functions. Leber congenital amaurosis (LCA) is clinically and genetically heterogeneous disease with autosomal recessive pattern of inheritance and is characterized by severe vision loss present at birth or early childhood. Up to now 19 genes have been identified in pathogenic course of LCA, but mut ...
... functions. Leber congenital amaurosis (LCA) is clinically and genetically heterogeneous disease with autosomal recessive pattern of inheritance and is characterized by severe vision loss present at birth or early childhood. Up to now 19 genes have been identified in pathogenic course of LCA, but mut ...
How different is anatomy?
... Gluconeogenesis Comparison is difficult, especially across species or across databases that each use one of these different variants Use a single term, and plenty of synonyms ...
... Gluconeogenesis Comparison is difficult, especially across species or across databases that each use one of these different variants Use a single term, and plenty of synonyms ...
Universal microbial diagnostics using random DNA probes
... The accurate, efficient, and rapid identification of microbial organisms, such as bacteria and viruses, is of mounting importance in the fields of health care, environmental monitoring, defense, and beyond (1–3). Sepsis from bacterial infection is currently the 11th leading cause of death in the Uni ...
... The accurate, efficient, and rapid identification of microbial organisms, such as bacteria and viruses, is of mounting importance in the fields of health care, environmental monitoring, defense, and beyond (1–3). Sepsis from bacterial infection is currently the 11th leading cause of death in the Uni ...
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... genome sequencing (WGS) or targeted enrichment using exome or gene panels. Copy number variation (CNV) of genomic segments is a large category of structural variation and has been implicated in many Mendelian diseases and complex traits. The impact of CNVs on gene expression is not limited to only t ...
... genome sequencing (WGS) or targeted enrichment using exome or gene panels. Copy number variation (CNV) of genomic segments is a large category of structural variation and has been implicated in many Mendelian diseases and complex traits. The impact of CNVs on gene expression is not limited to only t ...
Characterization of two rice DNA methyltransferases
... and cloned into pCR-Script Amp (SK+)™ (Stratagene) to generate an antisense construct, psM1/pPCR. An antisense riboprobe of 312 nucleotides (227 nucleotides of coding region plus 85 nucleotides of polylinker) was synthesized by in vitro transcription (MAXIscript™ T7/T3 Kit) (Ambion) using T3 RNA pol ...
... and cloned into pCR-Script Amp (SK+)™ (Stratagene) to generate an antisense construct, psM1/pPCR. An antisense riboprobe of 312 nucleotides (227 nucleotides of coding region plus 85 nucleotides of polylinker) was synthesized by in vitro transcription (MAXIscript™ T7/T3 Kit) (Ambion) using T3 RNA pol ...
Gene Section IGH (Immunoglobulin Heavy) Atlas of Genetics and Cytogenetics
... belonging to 7 subgroups, 9 IGHJ segments, and 11 IGHC genes. Eighty-two to 88 IGHV genes belong to 7 subgroups, whereas 41 pseudogenes, which are too divergent to be assigned to subgroups, have been assigned to 4 clans. Seven non-mapped IGHV genes have been described as insertion/deletion polymorph ...
... belonging to 7 subgroups, 9 IGHJ segments, and 11 IGHC genes. Eighty-two to 88 IGHV genes belong to 7 subgroups, whereas 41 pseudogenes, which are too divergent to be assigned to subgroups, have been assigned to 4 clans. Seven non-mapped IGHV genes have been described as insertion/deletion polymorph ...
Genome Evolution, Chromosomal Mutations, Paralogy
... • a net is a hierarchical collection of chains, with the highest-scoring non-overlapping chains on top, and their gaps filled in where possible by lower-scoring chains, for several levels. • a net is single-coverage for target but not for query. • because it's single-coverage in the target, it's no ...
... • a net is a hierarchical collection of chains, with the highest-scoring non-overlapping chains on top, and their gaps filled in where possible by lower-scoring chains, for several levels. • a net is single-coverage for target but not for query. • because it's single-coverage in the target, it's no ...
Evolutionary relationships of the Tas2r receptor gene families in
... partial sequences, two contained a frameshift each and 27 appeared to be full-length Tas2r genes. We aligned all known, publicly available, TAS2R receptor sequences and developed an HMM model characteristic of the TAS2R family to search in a database of protein translations of predicted mouse genes ...
... partial sequences, two contained a frameshift each and 27 appeared to be full-length Tas2r genes. We aligned all known, publicly available, TAS2R receptor sequences and developed an HMM model characteristic of the TAS2R family to search in a database of protein translations of predicted mouse genes ...
A Sex Chromosome Rearrangement in a Human XX
... pseudoautosomal sequences proximal to the breakpoint in U7should be present in three copies (one each from the paternal X, the paternal Y, and a maternal X chromosome). Those pseudoautosomal loci distal to U7 would be present in only two copies (one from the paternal Y chromosome and one from a mate ...
... pseudoautosomal sequences proximal to the breakpoint in U7should be present in three copies (one each from the paternal X, the paternal Y, and a maternal X chromosome). Those pseudoautosomal loci distal to U7 would be present in only two copies (one from the paternal Y chromosome and one from a mate ...
Molecular Evolution of the Avian CHD1 Genes on the Z
... Genes shared between the nonrecombining parts of the two types of sex chromosomes offer a potential means to study the molecular evolution of the same gene exposed to different genomic environments. We have analyzed the molecular evolution of the coding sequence of the first pair of genes found to b ...
... Genes shared between the nonrecombining parts of the two types of sex chromosomes offer a potential means to study the molecular evolution of the same gene exposed to different genomic environments. We have analyzed the molecular evolution of the coding sequence of the first pair of genes found to b ...
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use either ""shotgun"" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before.