Reveal—visual eQTL analytics
... if a conservative threshold is chosen. A popular stand-alone tool is WGAViewer (Ge et al., 2008) which offers an interactive Manhattan plot embedded into an annotation environment in order to help identify those associations with large biological relevance. Genevar (Yang et al., 2010) combines a dat ...
... if a conservative threshold is chosen. A popular stand-alone tool is WGAViewer (Ge et al., 2008) which offers an interactive Manhattan plot embedded into an annotation environment in order to help identify those associations with large biological relevance. Genevar (Yang et al., 2010) combines a dat ...
The Topology of the Possible
... conditions under which a phenotypic innovation can, once generated, invade an existing population. The classical fields of inquiry concerned with selection are population genetics and ecology. The main variables are frequencies of genes or species representatives whose change is typically described ...
... conditions under which a phenotypic innovation can, once generated, invade an existing population. The classical fields of inquiry concerned with selection are population genetics and ecology. The main variables are frequencies of genes or species representatives whose change is typically described ...
cached copy
... opposite page]. The stickiness is the propensity of the overhanging piece to bond with a matching strand that has the complementary bases in the corresponding order— the base adenine on one strand pairs with thymine on the opposite strand, and cytosine binds with guanine. At first sight, it does not ...
... opposite page]. The stickiness is the propensity of the overhanging piece to bond with a matching strand that has the complementary bases in the corresponding order— the base adenine on one strand pairs with thymine on the opposite strand, and cytosine binds with guanine. At first sight, it does not ...
The Complement of Enzymatic Sets in Different Species
... The correlation coefficients for the KEGG sets and the conservative sets are lower, but still significant at 0.90 and 0.79, respectively. The actual protein composition of the conservative and the KEGG sets in Escherichia coli almost completely overlaps. In addition, the reaction composition is more ...
... The correlation coefficients for the KEGG sets and the conservative sets are lower, but still significant at 0.90 and 0.79, respectively. The actual protein composition of the conservative and the KEGG sets in Escherichia coli almost completely overlaps. In addition, the reaction composition is more ...
An In Silico Investigation Into the Discovery of Novel Cis
... The intronic regions of the PAX7 gene were analyzed using computational DNA pattern recognition methods. Several potential cis-regulatory motifs were identified in this investigation and one in particular that was common to both PAX7 and PAX3 and also to NF1, could have implications for the role of ...
... The intronic regions of the PAX7 gene were analyzed using computational DNA pattern recognition methods. Several potential cis-regulatory motifs were identified in this investigation and one in particular that was common to both PAX7 and PAX3 and also to NF1, could have implications for the role of ...
RiboT
... RiboT is a fantastic molecule: a ribosome with tethered subunits, that is able to substain the expression of an entire genome! That’s incredible! So, what now? ...
... RiboT is a fantastic molecule: a ribosome with tethered subunits, that is able to substain the expression of an entire genome! That’s incredible! So, what now? ...
Political Science, Biometric Theory, and Twin Studies: A
... currently being used for political research by several political scientists (e.g., see Fowler and Dawes 2008). The population-based approach diminishes sample biases as much as possible, while providing the means to evaluate related individuals.2 Importantly, results from a single population should ...
... currently being used for political research by several political scientists (e.g., see Fowler and Dawes 2008). The population-based approach diminishes sample biases as much as possible, while providing the means to evaluate related individuals.2 Importantly, results from a single population should ...
A Major Species of Mouse μ-opioid Receptor mRNA and Its
... important role in gene regulation. The average length of 3⬘-UTR has increased dramatically throughout the evolutionary process, from 200 nucleotides in plant and fungi to 800 and more in humans and other vertebrates. This increase suggests a potential role of longer 3⬘-UTR in the regulation of more ...
... important role in gene regulation. The average length of 3⬘-UTR has increased dramatically throughout the evolutionary process, from 200 nucleotides in plant and fungi to 800 and more in humans and other vertebrates. This increase suggests a potential role of longer 3⬘-UTR in the regulation of more ...
Slide 1
... • Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. GREAT assigns biological meaning to a set of non-coding genomic regions by analyzing the annotations of the nearby genes. Thus, it is particularly useful in studying functions o ...
... • Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. GREAT assigns biological meaning to a set of non-coding genomic regions by analyzing the annotations of the nearby genes. Thus, it is particularly useful in studying functions o ...
The Co-Evolution of Genes and Culture Pedigrees and the
... lactase switch in several individuals. They found many differences. For example, at one particular position in the sequence of DNA, some individuals might have an adenine (A) nucleotide and others a thymine (T) nucleotide. Most of the differences in DNA sequence have no effect on lactase production. ...
... lactase switch in several individuals. They found many differences. For example, at one particular position in the sequence of DNA, some individuals might have an adenine (A) nucleotide and others a thymine (T) nucleotide. Most of the differences in DNA sequence have no effect on lactase production. ...
BIO 4333/6V29: DNA Replication, Recombination, and Repair
... two sequences share, as well as the percent similarity • The score of a pairwise alignment includes positive values for exact matches, and other scores for mismatches and gaps • PAM and BLOSUM matrices provide a set of rules for assigning scores. PAM10 and BLOSUM80 are matrices appropriate for the c ...
... two sequences share, as well as the percent similarity • The score of a pairwise alignment includes positive values for exact matches, and other scores for mismatches and gaps • PAM and BLOSUM matrices provide a set of rules for assigning scores. PAM10 and BLOSUM80 are matrices appropriate for the c ...
BLAST - UPCH
... two sequences share, as well as the percent similarity • The score of a pairwise alignment includes positive values for exact matches, and other scores for mismatches and gaps • PAM and BLOSUM matrices provide a set of rules for assigning scores. PAM10 and BLOSUM80 are matrices appropriate for the c ...
... two sequences share, as well as the percent similarity • The score of a pairwise alignment includes positive values for exact matches, and other scores for mismatches and gaps • PAM and BLOSUM matrices provide a set of rules for assigning scores. PAM10 and BLOSUM80 are matrices appropriate for the c ...
Slide 1
... This workflow simplifies a BLAST text file into identifiers, descriptions and values (P, E-values). In order to extract the relevant ids etc. you need to pass the relevant string into the corresponding port, e.g. the default port being used is gi. This has been passed "gi". For any other ports simpl ...
... This workflow simplifies a BLAST text file into identifiers, descriptions and values (P, E-values). In order to extract the relevant ids etc. you need to pass the relevant string into the corresponding port, e.g. the default port being used is gi. This has been passed "gi". For any other ports simpl ...
Chip-seq analysis
... Hint: Rename the datasets all along the training session. Q1: Is the number of aligned reads balanced ? Hint: when running twice the same tool with the same parameters on several datasets, you can use . Then, select all the datasets you want to analyse (select multiple datasets by pressing the Ctrl ...
... Hint: Rename the datasets all along the training session. Q1: Is the number of aligned reads balanced ? Hint: when running twice the same tool with the same parameters on several datasets, you can use . Then, select all the datasets you want to analyse (select multiple datasets by pressing the Ctrl ...
Research Article Reservoir of Bacterial Exotoxin Genes in the
... 2.3. Characterization of the sea PCR Product. Sequencing of the sea PCR product obtained from the environmental isolate generated a 280 bp DNA sequence. The nucleotide composition of the amplified sequence was analyzed using BioEdit [34]. The sequence of the amplified PCR product contained a G + C c ...
... 2.3. Characterization of the sea PCR Product. Sequencing of the sea PCR product obtained from the environmental isolate generated a 280 bp DNA sequence. The nucleotide composition of the amplified sequence was analyzed using BioEdit [34]. The sequence of the amplified PCR product contained a G + C c ...
The hybrid origins of three perennial Medicago species
... The output from the MiSeq instrument is c. 350 000 paired-end reads of 150 bp at each end, resulting in a total of 11 Gb of sequence across all 52 samples per sequencing run. The reads were assembled into contigs for each gene and each individual using the CLC Genomics software (CLC Bio, Aarhus, Den ...
... The output from the MiSeq instrument is c. 350 000 paired-end reads of 150 bp at each end, resulting in a total of 11 Gb of sequence across all 52 samples per sequencing run. The reads were assembled into contigs for each gene and each individual using the CLC Genomics software (CLC Bio, Aarhus, Den ...
Characterization of the neurohypophysial hormone gene loci in
... Background: Vasopressin and oxytocin are mammalian neurohypophysial hormones with distinct functions. Vasopressin is involved mainly in osmoregulation and oxytocin is involved primarily in parturition and lactation. Jawed vertebrates contain at least one homolog each of vasopressin and oxytocin, whe ...
... Background: Vasopressin and oxytocin are mammalian neurohypophysial hormones with distinct functions. Vasopressin is involved mainly in osmoregulation and oxytocin is involved primarily in parturition and lactation. Jawed vertebrates contain at least one homolog each of vasopressin and oxytocin, whe ...
MICROBIAL EXPOSURE, SYMPTOMS AND INFLAMMATORY
... Aspergillus fumigatus, A. versicolor, and A. niger were identified to species level. Total numbers of bacterial colonies were counted after 5 days of incubation (20oC) and the number of actinomycete colonies was counted from the bacteria plates after 14 days. Surface and material sampling. In the kit ...
... Aspergillus fumigatus, A. versicolor, and A. niger were identified to species level. Total numbers of bacterial colonies were counted after 5 days of incubation (20oC) and the number of actinomycete colonies was counted from the bacteria plates after 14 days. Surface and material sampling. In the kit ...
... The genus Saccharomyces consists of seven biological species: S. arboricolus, S. bayanus, S. cariocanus, S. cerevisiae, S. kudriavzevii, S. mikatae, and S. paradoxus (29, 59) and the partially allotetraploid species S. pastorianus (46, 58). The hybrid species S. pastorianus, restricted to lager brew ...
pdf
... Magical taxa were chosen based on those samples contained in Newt Scamander’s personal collection, as well as those found in the Magizoological Museum at the Ministry of Magic. Some samples could not be used, as they were too degraded for DNA extraction. Non-magical taxa were chosen based on descrip ...
... Magical taxa were chosen based on those samples contained in Newt Scamander’s personal collection, as well as those found in the Magizoological Museum at the Ministry of Magic. Some samples could not be used, as they were too degraded for DNA extraction. Non-magical taxa were chosen based on descrip ...
Lampetra fluviatilis Neurotrophin Homolog, Descendant of a
... gene family that dates back more than 460 million years to the early vertebrate ancestors. The results show that the neurotrophin gene family was originally formed by two subsequent duplications. The duplication that formed nerve growth factor, neurotrophin-3, brain-derived neurotrophic factor, and ...
... gene family that dates back more than 460 million years to the early vertebrate ancestors. The results show that the neurotrophin gene family was originally formed by two subsequent duplications. The duplication that formed nerve growth factor, neurotrophin-3, brain-derived neurotrophic factor, and ...
Ugandan Kaposi`s Sarcoma-Associated Herpesvirus Phylogeny
... molecular processes by which these distributions arose. As has been proposed for other viruses [38, 39], Hayward et al. [6] hypothesized that KSHV is an evolutionarily old human virus distributed worldwide along broad ethnic and geographic lines and acts as a marker for ancient human migration. At t ...
... molecular processes by which these distributions arose. As has been proposed for other viruses [38, 39], Hayward et al. [6] hypothesized that KSHV is an evolutionarily old human virus distributed worldwide along broad ethnic and geographic lines and acts as a marker for ancient human migration. At t ...
Whole genome analyses using PopGenome and VCF files
... This module provides a wide range of FST as well as diversity measurenments. There exists two main classes. First, calculations which are either based on haplotypes mode=ḧaplotype¨ or second, the sequence based methods focussing on nucleotides mode="nucleotide". Note, be careful with haplotype base ...
... This module provides a wide range of FST as well as diversity measurenments. There exists two main classes. First, calculations which are either based on haplotypes mode=ḧaplotype¨ or second, the sequence based methods focussing on nucleotides mode="nucleotide". Note, be careful with haplotype base ...
Title: Evolution of dosage compensation in Anolis carolinensis, a
... genotyping of all 20 samples using GATK’s GenotypeGVCFs with default parameters. We calculated genetic diversity within each set of biological replicates. For example, population 1 consisted of biological replicate 1 for each of the four individuals, population 2 consisted of biological replicate 2 ...
... genotyping of all 20 samples using GATK’s GenotypeGVCFs with default parameters. We calculated genetic diversity within each set of biological replicates. For example, population 1 consisted of biological replicate 1 for each of the four individuals, population 2 consisted of biological replicate 2 ...
Insights into three whole-genome duplications gleaned
... estimated gaps) is composed of 1,202 scaffolds, 274 of which have lengths >2 kb and 96 of which are >50 kb (Table S1). This is less than half the genome size of all members of the P. aurelia complex that have been sequenced (68-77 Mb) (McGrath et al., submitted), and consistent with P. caudatum havi ...
... estimated gaps) is composed of 1,202 scaffolds, 274 of which have lengths >2 kb and 96 of which are >50 kb (Table S1). This is less than half the genome size of all members of the P. aurelia complex that have been sequenced (68-77 Mb) (McGrath et al., submitted), and consistent with P. caudatum havi ...
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.