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Showing 1 to 20 of 37 for “"DNA sequence analysis"”.
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Some Probability Methods For DNA Sequence Analysis
Probability models are employed in the analysis of data emerging from DNA sequence studies. To sequence DNA sequences, one of the methods employed is to sequence overlapping fragments of the DNA. These overlapping fragments form a contig. In this thesis, probability methods to study the mean number …
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RNA and DNA Sequence Analysis of the Human Transcriptome
… part by gene expression, or the transcription of DNA into RNA. As such, the study of the transcriptome, or the characterization and quantification of all RNA produced in the cell, is important. Recent advances in sequencing technology have allowed for unprecedented interrogation of the …
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Characterization, purification, and DNA sequence analysis of a novel ATPase of the archaebacterium Methanococcus voltae
Membrane-bound ATPase activity was detected in the methanogen Methanococcus voltae. The ATPase was inhibited by vanadate, a characteristic inhibitor of the P type ATPases. The enzyme activity was also inhibited by diethylstilbestrol. However, it was insensitive to …
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A preliminary study of genetic variation within and among populations of Diaptomus leptopus (Copepoda: Calanoida) : a DNA sequence analysis of the Mitochondrial Cytochrome Oxidase I gene
… morphological traits and allozyme studies. DNA sequence analysis of the mitochondrial cytochrome oxidase I gene may also be of use to study population structure. Thus, a study investigating the genetic variation within and among seven populations, distributed from Quebec to New York, of the …
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Minimizer-space computation
As the volume of DNA sequencing data increases, the need for algorithmic advances to efficiently handle the data arises. One such concept is minimizers, which are genomic substrings that allow for reduced representations of larger DNA sequences. In this thesis, we introduce minimizer-space …
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Study of the baiE Gene in Bile Acid 7α-Dehydroxylating Bacteria
… tested showed amplification at the predicted DNA fragment size. Partial DNA sequence analysis of the amplified baiE-like genes revealed 88-95% homology with the baiE gene of Eubacterium sp.V.P.I. 12708. These data suggest that baiE-like genes are present in the five bile acid …
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Molecular phylogeographic structure within the Perognathus fasciatus species-group
… P. fasciatus, P. flavescens, and P. apache. DNA sequence analysis of mitochondrial DNA (mtDNA) revealed that these three species comprise a monophyletic clade relative to other species of Perognathus. MtDNA sequence divergence and nucleotide diversity are much higher within populations of P. …
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Characterization of the Genes Involved in Biosynthesis and Transport of Schizokinen, a Siderophore Produced by <em>Rhizobium leguminosarum</em> IARI 917.
… biosynthesis using mini Tn5 random mutagenesis. DNA sequence analysis of a non siderophore producing transconjugant revealed a gene involved in PAC/PAS signal transduction systems that respond to many extracellular cues.</p>
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Study of the baiG Gene in Bile Acid 7α-Dehydroxylating Bacteria
… in two of the bacterial strains at the predicted DNA fragment size. Partial DNA sequence analysis of the amplified baiG-like gene fragments revealed 96-97% homology with the baiG gene of Eubacterium sp. strain V.P.I. 12708. These data suggest that baiG-like genes are present in Clostridium sp. …
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Association of <i>glpQ</i> with serum-resistance in <i>salmonella typhimurium</i>
… serum-resistance. Inverse PCR and subsequent DNA sequence analysis reveal the insertion to be in the gene <em>glpQ</em>. <em>glpQ</em> codes for a periplasmic glycerophosphodiester phosphodiesterase involved in glycerol degradation. Complementation assays using a clone of <em>glpQ</em> on a …
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Molecular Analysis of a Cellulase/xylanase gene,celD, From the Ruminal Bacterium Ruminococcus Flavefaciens Fd-1
… library of Ruminococcus flavefaciens FD-1 DNA was constructed using the Escherichia coli bacteriophage $\lambda$ vector $\lambda$DASH. A recombinant phage exhibiting activity against both Ostazin brilliant red-hydroxyethyl cellulose and carboxymethyl cellulose (CMC) was isolated. This clone …
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Molecular Biology of the Cytochrome O Terminal Oxidase of Escherichia Coli (Cloning, Sequencing, Dna)
… gene locus is located in a 5.5-kb chromosomal DNA segment. The nucleotide sequence of a portion of the cyo gene locus has been determined by Sanger's dideoxynucleotide sequencing method. Further genetic manipulations and a complete DNA sequence analysis of the cyo gene locus will provide …
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Molecular, genetic, and biochemical studies of mannityl opine utilization by Agrobacterium tumefaciens: Its evolutionary implications
… as fast on this opine as does wild type cells. DNA sequence analysis of the region necessary for utilization of these opines revealed seven putative genes; moc (manniyl opine catabolism) D and E, oriented from right to left, and $mocRCBAR\sp\prime$, from left to right. MocD is a homologue of the …
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An analysis of human Alu element lineages
… elements that reside in the human genome draft sequence and focused our analyses on the 4051 autosomal Alu elements. A total of 2672 autosomal loci were subjected to polymerase chain reaction (PCR)-based assays that allow analysis of individual elements for insertion presence and absence. The …
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An Efficient Primer Selection Process Combining Progressive and Iterative Multiple Sequence Alignment Strategies: ClustalW and HMMER
… efficient algorithm to identify candidate DNA primer sequences. DNA sequencing primers are a critical element of polymerase chain reaction (PCR) and DNA sequence analysis. A variety of methods for deriving DNA primers exist, but such methods are often computationally intensive, or do not …
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Cloning, High-Level Expression, and Characterization of Escherichia Coli Cytochrome B(562)
… full length gene, including the promotor. The DNA sequence analysis of the gene revealed the presence of a leader sequence, with the characteristics of an E. coli signal sequence, in front of the coding sequences for the mature protein. Localization studies on the overexpressed protein revealed …
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Validation of a Pan-fungal polymerase chain reaction (PCR) assay for the detection and identification of medically important fungi in a diagnostic laboratory
… identified reference fungal isolates. The DNA yield and purity of three different DNA extraction methods was assessed, using 6 representative fungal isolates. The ZR Fungal/Bacterial DNA MicroPrep™ produced a median concentration of 17.28 ng/μl,which was significantly higher (p value = …
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Entropy-based machine learning algorithms applied to genomics and pattern recognition
… factors (TF) are proteins that interact with DNA to regulate the transcription of DNA to RNA and play key roles in both healthy and cancerous cells. Thus, gaining a deeper understanding of the biological factors underlying transcription factor (TF) binding specificity is important for …
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Stability of Nucleic Acid Secondary Structures and Their Contribution to Gene Expression
… encoded in the bacterio-opsin gene {bop) (1). DNA sequence analysis and predictive folding algorithms suggest that the first twenty-five bases of the bop gene mRNA can form a secondary structural element (a "stem-loop"). Using biophysical methods, the goal was to determine if the stem-loop …
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Identification and characterization of the ribosomal RNA operons from Rhodobacter sphaeroides
… sphaeroides were identified, cloned and sequenced. DNA sequence analysis has identified the 16S, 23S and 5S rRNAs, two tRNAs (ile and ala) in the 16S-23S spacer region, and an f-met tRNA immediately following the 5S rRNa gene of all three operons. The secondary structure of the rRNA and …
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