Guide to Seq. Annotation - UC Davis Plant Sciences
... genes. They usually appear as similar (aligned) segments (exons) separated by non similar ones (introns) If you do not find anything with BLASTN you can do a more sensitive search using BLASTX, which will translate your DNA and search the protein databases, which is more sensitive for more distantly ...
... genes. They usually appear as similar (aligned) segments (exons) separated by non similar ones (introns) If you do not find anything with BLASTN you can do a more sensitive search using BLASTX, which will translate your DNA and search the protein databases, which is more sensitive for more distantly ...
File S1.
... as long as it has at least a coverage of one, and the maximum allowed gap is not exceeded. A coverage of one is used to identify the largest possible fragmet size. If a region cannot be exceeded anymore because there is no more coverage, it is tested whether it meets the other criteria given. These ...
... as long as it has at least a coverage of one, and the maximum allowed gap is not exceeded. A coverage of one is used to identify the largest possible fragmet size. If a region cannot be exceeded anymore because there is no more coverage, it is tested whether it meets the other criteria given. These ...
Part 1 Microarray Timeseries Analysis with replicates OSM
... The test statistic used for the gene-set-test is the mean of the statistics in the set. If ranks.only is TRUE the only the ranks of the statistics are used. In this case the pvalue is obtained from a Wilcoxon test. If ranks.only is FALSE, then the p-value is obtained by simulation using nsim random ...
... The test statistic used for the gene-set-test is the mean of the statistics in the set. If ranks.only is TRUE the only the ranks of the statistics are used. In this case the pvalue is obtained from a Wilcoxon test. If ranks.only is FALSE, then the p-value is obtained by simulation using nsim random ...
identifying parent-daughter relationships among duplicated genes1
... node. We paired each human gene and each macaque gene within a family to assemble the dataset. For each gene, we downloaded the ±10 MB flanking region from Ensembl and extracted the gene order by encoding the genes according to the gene family IDs defined in Ensembl. We chose the length of the flank ...
... node. We paired each human gene and each macaque gene within a family to assemble the dataset. For each gene, we downloaded the ±10 MB flanking region from Ensembl and extracted the gene order by encoding the genes according to the gene family IDs defined in Ensembl. We chose the length of the flank ...
National Newborn Bloodspot Screening Programme
... A baby who carries CF must have inherited one altered gene from one parent. This means that either Mum or Dad also carries CF. However, it is possible that BOTH Mum and Dad carriers carry CF and, purely by chance, did not have a child with cystic fibrosis on this occasion. If both parents carry CF, ...
... A baby who carries CF must have inherited one altered gene from one parent. This means that either Mum or Dad also carries CF. However, it is possible that BOTH Mum and Dad carriers carry CF and, purely by chance, did not have a child with cystic fibrosis on this occasion. If both parents carry CF, ...
Article Comparative Genomics as a Time Machine: How Relative
... Using a phylogenetic model of evolution after genome duplication (i.e., polyploidy) and 12 yeast genomes with a shared genome duplication, I show that the loss of duplicate genes after that duplication occurred in three phases. First, losses that occurred immediately after the event were biased towa ...
... Using a phylogenetic model of evolution after genome duplication (i.e., polyploidy) and 12 yeast genomes with a shared genome duplication, I show that the loss of duplicate genes after that duplication occurred in three phases. First, losses that occurred immediately after the event were biased towa ...
TURNING PAGES
... with DNA and with bacterial and bacteriophage mutants (and, as a concurrent sabbatical activity, learned to fly!). Then, when Fred’s Charon bacteriophages were judged to be safe enough for use in cloning human genes, our groups collaborated in isolating and characterizing the two closely related gen ...
... with DNA and with bacterial and bacteriophage mutants (and, as a concurrent sabbatical activity, learned to fly!). Then, when Fred’s Charon bacteriophages were judged to be safe enough for use in cloning human genes, our groups collaborated in isolating and characterizing the two closely related gen ...
What causes Evolution?
... Distribution of "minor-allele" counts for mt hypervariable region 2 nucleotides in Africans, Asians, and Europeans. The X-axis indicates the copy number of each minor allele in each population (i.e., whether the allele is seen once, twice, etc.), and the Y-axis indicates the number of alleles ...
... Distribution of "minor-allele" counts for mt hypervariable region 2 nucleotides in Africans, Asians, and Europeans. The X-axis indicates the copy number of each minor allele in each population (i.e., whether the allele is seen once, twice, etc.), and the Y-axis indicates the number of alleles ...
A Separate Peace – Pre
... Although Gene does not want to attend meetings of the “Super Suicide Society,” he attends the meetings, stating, “Otherwise, I would have lost face with Phineas, and that would have been unthinkable.” What does this tell us about Gene’s attitude towards Phineas? How important is Phineas to Gene’ ...
... Although Gene does not want to attend meetings of the “Super Suicide Society,” he attends the meetings, stating, “Otherwise, I would have lost face with Phineas, and that would have been unthinkable.” What does this tell us about Gene’s attitude towards Phineas? How important is Phineas to Gene’ ...
doc - Sol Genomics Network
... (pepper etc). BAC analysis shows that gene order is highly conserved between the sol species, even some (more complex) ordering is preserved in arabadopsis. ...
... (pepper etc). BAC analysis shows that gene order is highly conserved between the sol species, even some (more complex) ordering is preserved in arabadopsis. ...
AIR Inquiry
... CRISPR-Cas genome editing is an in vivo DNA double-strand break (DSB) technology based on a bacterial endonuclease called Cas9. It utilizes a combination of protein-DNA and RNA-DNA pairing to direct targeted double strand breaks in the DNA sequence of interest. Cas9 endonuclease is guided to a targe ...
... CRISPR-Cas genome editing is an in vivo DNA double-strand break (DSB) technology based on a bacterial endonuclease called Cas9. It utilizes a combination of protein-DNA and RNA-DNA pairing to direct targeted double strand breaks in the DNA sequence of interest. Cas9 endonuclease is guided to a targe ...
Updated map of duplicated regions in the yeast genome
... shown in Fig. 2. It should be noted that approximately 11 of these are expected to be artefactual. The revised map includes 39 tRNA gene pairs as well as one snRNA gene pair (SNR17A/SNR17B; Hughes et al., 1987). A tRNA gene was included in the map if it occurred within a block and had a homolog loca ...
... shown in Fig. 2. It should be noted that approximately 11 of these are expected to be artefactual. The revised map includes 39 tRNA gene pairs as well as one snRNA gene pair (SNR17A/SNR17B; Hughes et al., 1987). A tRNA gene was included in the map if it occurred within a block and had a homolog loca ...
Gene duplication and divergence in the early evolution of
... by acquisition of further functions C and D. It is important to recognise that these models are not mutually exclusive. It is likely that all are correct to some degree and all occur to some extent, but there may be variations according to taxon, type of gene and type of duplication. The important q ...
... by acquisition of further functions C and D. It is important to recognise that these models are not mutually exclusive. It is likely that all are correct to some degree and all occur to some extent, but there may be variations according to taxon, type of gene and type of duplication. The important q ...
Document
... 1. More heat shock and stress-responsive genes (ex. those coding for heat shock proteins and chaperons) are highly expressed at 48˚C than are at lower temperatures, indicating that the fungus is under heat stress. 2. More putative virulence genes (ex. those coding for the proteins responsive to ox ...
... 1. More heat shock and stress-responsive genes (ex. those coding for heat shock proteins and chaperons) are highly expressed at 48˚C than are at lower temperatures, indicating that the fungus is under heat stress. 2. More putative virulence genes (ex. those coding for the proteins responsive to ox ...
Supplementary Figure Legends - Word file
... promoter activation. A simplistic display of a P.falciparum nucleus divided into the transcriptionally incompetent nuclear periphery (red) and a transcriptionally active central region (green) that extends to the nuclear membrane at one site. This previously described active perinuclear zone1 includ ...
... promoter activation. A simplistic display of a P.falciparum nucleus divided into the transcriptionally incompetent nuclear periphery (red) and a transcriptionally active central region (green) that extends to the nuclear membrane at one site. This previously described active perinuclear zone1 includ ...
Welcome to the Broad Institute
... • To change the parameters and/or assumptions, download the data and analyze it in GenePattern directly • Detailed descriptions of the analyses, how to run them, and ...
... • To change the parameters and/or assumptions, download the data and analyze it in GenePattern directly • Detailed descriptions of the analyses, how to run them, and ...
Hardy-Weinberg Lab
... report that includes the species’ classification scheme, the research journal in which the gene was first reported, and the sequence of bases that appear to align with your gene of interest. 11. Click on the link titled “Distance tree of results,” to see a cladogram with the species with similar seq ...
... report that includes the species’ classification scheme, the research journal in which the gene was first reported, and the sequence of bases that appear to align with your gene of interest. 11. Click on the link titled “Distance tree of results,” to see a cladogram with the species with similar seq ...
Statistics and bioinformatics applied to omics
... • It is harder to obtain biological understanding from this data. • One strategy: consider the functional annotation of the differentially expressed genes. • Question: what do these genes have in common that could be of interest ? ...
... • It is harder to obtain biological understanding from this data. • One strategy: consider the functional annotation of the differentially expressed genes. • Question: what do these genes have in common that could be of interest ? ...
Genetic Inheritance - Wesleyan Science Outreach
... their kids, we get one gene from mom and one gene from dad to make what we look like! Let’s think for a moment. Do your parents look like you? What about your grandparents, relatives? Does everyone in your family look alike? Why do you think that is or isn’t? No one gets to choose the genes they ...
... their kids, we get one gene from mom and one gene from dad to make what we look like! Let’s think for a moment. Do your parents look like you? What about your grandparents, relatives? Does everyone in your family look alike? Why do you think that is or isn’t? No one gets to choose the genes they ...
Copy-number variation
Copy-number variations (CNVs)—a form of structural variation—are alterations of the DNA of a genome that results in the cell having an abnormal or, for certain genes, a normal variation in the number of copies of one or more sections of the DNA. CNVs correspond to relatively large regions of the genome that have been deleted (fewer than the normal number) or duplicated (more than the normal number) on certain chromosomes. For example, the chromosome that normally has sections in order as A-B-C-D might instead have sections A-B-C-C-D (a duplication of ""C"") or A-B-D (a deletion of ""C"").This variation accounts for roughly 13% of human genomic DNA and each variation may range from about one kilobase (1,000 nucleotide bases) to several megabases in size. CNVs contrast with single-nucleotide polymorphisms (SNPs), which affect only one single nucleotide base.