computation for chIP-seq and rNA-seq studies
... that map to a unique position in the genome or can include ‘multireads’ that map to multiple sites). These early choices in the analysis affect sensitivity and specificity, and their effects vary based on the specifics of each genome. If only uniquely mapping reads are used, some true sites of occup ...
... that map to a unique position in the genome or can include ‘multireads’ that map to multiple sites). These early choices in the analysis affect sensitivity and specificity, and their effects vary based on the specifics of each genome. If only uniquely mapping reads are used, some true sites of occup ...
Translation
... → the large subunit binds (ribosome is completed) while the initiator tRNA is bound at the P site → further aminoacyl-tRNA, with the anticodon corresponding to the second codon of mRNA after AUG, binds at the A site [FIG.] ...
... → the large subunit binds (ribosome is completed) while the initiator tRNA is bound at the P site → further aminoacyl-tRNA, with the anticodon corresponding to the second codon of mRNA after AUG, binds at the A site [FIG.] ...
Elongation and Termination of Transcription
... – In Drosophila, the RNA polymerase can pause after synthesizing ~ 25 nucleotides of RNA in many genes. – under elevated temperature conditions, the heat shock factor stimulates elongation by release from pausing. – Other possible examples: mammalian c-myc, HIV LTR • This is in addition to regulatio ...
... – In Drosophila, the RNA polymerase can pause after synthesizing ~ 25 nucleotides of RNA in many genes. – under elevated temperature conditions, the heat shock factor stimulates elongation by release from pausing. – Other possible examples: mammalian c-myc, HIV LTR • This is in addition to regulatio ...
Translation
... → the large subunit binds (ribosome is completed) while the initiator tRNA is bound at the P site → further aminoacyl-tRNA, with the anticodon corresponding to the second codon of mRNA after AUG, binds at the A site [FIG.] ...
... → the large subunit binds (ribosome is completed) while the initiator tRNA is bound at the P site → further aminoacyl-tRNA, with the anticodon corresponding to the second codon of mRNA after AUG, binds at the A site [FIG.] ...
Full Text PDF - Mary Ann Liebert, Inc. publishers
... with yeast artificial chromosomes (YACs) covering the whole mouse tyrosinase locus totally rescues the hypopigmented phenotype and the retinal abnormalities associated with albinism (Schedl et al., 1993; Jeffery et al., 1994, 1997). These results clearly indicated the existence of important regulato ...
... with yeast artificial chromosomes (YACs) covering the whole mouse tyrosinase locus totally rescues the hypopigmented phenotype and the retinal abnormalities associated with albinism (Schedl et al., 1993; Jeffery et al., 1994, 1997). These results clearly indicated the existence of important regulato ...
Translation
... → the large subunit binds (ribosome is completed) while the initiator tRNA is bound at the P site → further aminoacyl-tRNA, with the anticodon corresponding to the second codon of mRNA after AUG, binds at the A site [FIG.] ...
... → the large subunit binds (ribosome is completed) while the initiator tRNA is bound at the P site → further aminoacyl-tRNA, with the anticodon corresponding to the second codon of mRNA after AUG, binds at the A site [FIG.] ...
Chapter 27 Phage Strategies
... • bacteriophage (or phage) – A bacterial virus. • lytic infection – Infection of a bacterium by a phage that ends in the destruction of the bacterium with release of progeny phage. • lysis – The death of bacteria at the end of a phage infective cycle when they burst open to release the progeny of an ...
... • bacteriophage (or phage) – A bacterial virus. • lytic infection – Infection of a bacterium by a phage that ends in the destruction of the bacterium with release of progeny phage. • lysis – The death of bacteria at the end of a phage infective cycle when they burst open to release the progeny of an ...
Interacting Gene Clusters and the Evolution of the Vertebrate
... have reported nonrandom gene order on eukaryotic genomes (Hurst et al. 2004). It has been reported that neighboring genes are coexpressed in Saccharomyces cerevisiae, Drosophila melanogaster, and C. elegans (Cohen et al. 2000; Spellman and Rubin 2002; Lercher et al. 2003). In addition, housekeeping ...
... have reported nonrandom gene order on eukaryotic genomes (Hurst et al. 2004). It has been reported that neighboring genes are coexpressed in Saccharomyces cerevisiae, Drosophila melanogaster, and C. elegans (Cohen et al. 2000; Spellman and Rubin 2002; Lercher et al. 2003). In addition, housekeeping ...
High mutation rates in human and ape pseudoautosomal genes
... another human pseudoautosomal gene, SHOX, is not higher than elsewhere in the genome (May et al., 2002). A noncoding pseudoautosomal region close to the Xp/Yp telomere was reported to have a high substitution rate (Cooke et al., 1985; Baird and Royle, 1997), however, subtelomeric regions are known t ...
... another human pseudoautosomal gene, SHOX, is not higher than elsewhere in the genome (May et al., 2002). A noncoding pseudoautosomal region close to the Xp/Yp telomere was reported to have a high substitution rate (Cooke et al., 1985; Baird and Royle, 1997), however, subtelomeric regions are known t ...
Codon usage and lateral gene transfer in Bacillus subtilis Ivan
... for high accuracy of translation. Dix and Thompson [30] have shown that indeed accuracy can heavily depend on a given codon. In particular, they have shown that the efficient UUC codon is less accurate than UUU, but preferred in highly expressed genes (class II genes), indicating that there has not ...
... for high accuracy of translation. Dix and Thompson [30] have shown that indeed accuracy can heavily depend on a given codon. In particular, they have shown that the efficient UUC codon is less accurate than UUU, but preferred in highly expressed genes (class II genes), indicating that there has not ...
Functional and ecological impacts of horizontal gene transfer in
... environments is well known. This is exemplified by the high level of HGT observed in the genome of the thermoacidophile Thermotoga, which has acquired genes relating to its environment and metabolism from archaebacteria inhabiting similar environments [30,31]. The possible role of HGT in adapting to ...
... environments is well known. This is exemplified by the high level of HGT observed in the genome of the thermoacidophile Thermotoga, which has acquired genes relating to its environment and metabolism from archaebacteria inhabiting similar environments [30,31]. The possible role of HGT in adapting to ...
Fusion Detection using Archer Analysis
... PCR duplicates which is important for many aspects of fusion and mutation detection. Fusion Detection in Archer™ Analysis Software ...
... PCR duplicates which is important for many aspects of fusion and mutation detection. Fusion Detection in Archer™ Analysis Software ...
B. thuringiensis kurstaki
... Chemical insecticides were found to lack specificity; consequently, beneficial insects were being killed along with those that were considered to be pests. Some times the natural enemies of the insect pest species were killed more efficiently than the target organisms. Given all the drawbacks associ ...
... Chemical insecticides were found to lack specificity; consequently, beneficial insects were being killed along with those that were considered to be pests. Some times the natural enemies of the insect pest species were killed more efficiently than the target organisms. Given all the drawbacks associ ...
Multifractal analysis of DNA sequences using a novel chaos
... two of them on the 1=f spectrum of DNA sequences [3]. By mapping the sequence onto a (1D) walk, Peng and others have built a kind of interface, whose statistics were used to probe the range of correlation of the sequences [4,5]. Linguistic features were claimed to have been found in noncoding DNA s ...
... two of them on the 1=f spectrum of DNA sequences [3]. By mapping the sequence onto a (1D) walk, Peng and others have built a kind of interface, whose statistics were used to probe the range of correlation of the sequences [4,5]. Linguistic features were claimed to have been found in noncoding DNA s ...
Supplementary Notes S1 (doc 64K)
... regions in the input list. Overlaps and duplicates in the initial lists were resolved and resulted in a final list of 11,000 target chromosomal regions, mostly corresponding to exons. 3. Add flanking sequence to uniform length of 1200 bp in size. Flanking regions were added to all regions less than ...
... regions in the input list. Overlaps and duplicates in the initial lists were resolved and resulted in a final list of 11,000 target chromosomal regions, mostly corresponding to exons. 3. Add flanking sequence to uniform length of 1200 bp in size. Flanking regions were added to all regions less than ...
Do nonasterid holoparasitic flowering plants have plastid genomes?
... ences to be visualized on agarose gels. For mitochondrial SSU rRNA, two regions associated with helix 6 and 43 account for most of the size increases whereas helix 9 is truncated and helix 10 is absent. Finally, distinct and characteristic SSU sequences from each of the three subcellular genomes hav ...
... ences to be visualized on agarose gels. For mitochondrial SSU rRNA, two regions associated with helix 6 and 43 account for most of the size increases whereas helix 9 is truncated and helix 10 is absent. Finally, distinct and characteristic SSU sequences from each of the three subcellular genomes hav ...
... shapes and colors that appear to be visited by different insects. The anthocyanin2 (an2) locus, a regulator of the anthocyanin biosynthetic pathway, is the main determinant of color differences. Here, we report an analysis of molecular events at the an2 locus that occur during Petunia spp evolution. ...
Drosophila - The Solomon H Snyder Department of Neuroscience
... segments might be rearranged by a particular insertion such as an FRT site; 4) which gene might be overexpressed by an inserted regulatory element; or 5) the location of a transgene for recombination with other genetic elements, such as a mutation or other transgenes. Since transposon integrated tra ...
... segments might be rearranged by a particular insertion such as an FRT site; 4) which gene might be overexpressed by an inserted regulatory element; or 5) the location of a transgene for recombination with other genetic elements, such as a mutation or other transgenes. Since transposon integrated tra ...
Acquisition of 1,000 eubacterial genes physiologically transformed a
... lineage, 162 of which (15%) have been retained in all 10 haloarchaeans sampled. The Ms, Mc, and Mm lineages have—like the haloarchaea—independently acquired hundreds of eubacterial genes, but the crucial observation is that they have remained strict anaerobes, and they have furthermore remained obli ...
... lineage, 162 of which (15%) have been retained in all 10 haloarchaeans sampled. The Ms, Mc, and Mm lineages have—like the haloarchaea—independently acquired hundreds of eubacterial genes, but the crucial observation is that they have remained strict anaerobes, and they have furthermore remained obli ...
Exercise II - GEP Community Server
... ii. inaccurate transcriptional start and termination sites and therefore inaccurate 5’- and 3’untranslated regions (caused by difficulties predicting first and last exons due to transcriptional start and termination sites not following easily discernable patterns). 8. The Augustus gene prediction ha ...
... ii. inaccurate transcriptional start and termination sites and therefore inaccurate 5’- and 3’untranslated regions (caused by difficulties predicting first and last exons due to transcriptional start and termination sites not following easily discernable patterns). 8. The Augustus gene prediction ha ...
A Feeling for the Organism Book Report Worksheet
... McClintock’s research led her to the understanding of transposition of genetic elements. However, she was ahead of her time and her thorough presentation of the concept was not well received by the scientific community in the 1950s. Many of her colleagues found her ideas and explanations too elusive ...
... McClintock’s research led her to the understanding of transposition of genetic elements. However, she was ahead of her time and her thorough presentation of the concept was not well received by the scientific community in the 1950s. Many of her colleagues found her ideas and explanations too elusive ...
a nine-base pair deletion distinguishes two en/spm
... sequence represents the parental type and the a1-m (papu) is a derived type. [The molecular differences between al-m(dense) and al-m(Au) could not be determined as al-m(dense) is not available]. Origin of the 9-base pair deletion. How the deletion occurred is not known since no detectable change occ ...
... sequence represents the parental type and the a1-m (papu) is a derived type. [The molecular differences between al-m(dense) and al-m(Au) could not be determined as al-m(dense) is not available]. Origin of the 9-base pair deletion. How the deletion occurred is not known since no detectable change occ ...
Peer-reviewed Article PDF
... through a mechanism analogous to RNAi [7]. In 2007, Barrangou and Horvath (food industry scientists at Danisco) and Moineau's group at Université Laval showed that spacer DNA could be used to alter the resistance of S. thermophilus to phage attack [8] S. thermophilus is widely used in the dairy indu ...
... through a mechanism analogous to RNAi [7]. In 2007, Barrangou and Horvath (food industry scientists at Danisco) and Moineau's group at Université Laval showed that spacer DNA could be used to alter the resistance of S. thermophilus to phage attack [8] S. thermophilus is widely used in the dairy indu ...
X chromosome gene expression in human tissues
... particular, for the 27 X-linked genes previously reported by Carrel and Willard [2] to escape inactivation (i.e., using the somatic cell hybrid system), Nguyen and Disteche [16] found a significant increase in expression in females for only a few of these escaped genes. Because of a paucity of femal ...
... particular, for the 27 X-linked genes previously reported by Carrel and Willard [2] to escape inactivation (i.e., using the somatic cell hybrid system), Nguyen and Disteche [16] found a significant increase in expression in females for only a few of these escaped genes. Because of a paucity of femal ...
DNA Sequence Capture and Enrichment by Microarray Followed by
... management of massive amounts of data and potential interference from highly homologous sequences (e.g., pseudogenes) (10 ). Because the NGS technology is so new, QC of the sequence data (including the accuracy of reads, quality scores for reads, and sequencingcoverage needs) has not yet been well d ...
... management of massive amounts of data and potential interference from highly homologous sequences (e.g., pseudogenes) (10 ). Because the NGS technology is so new, QC of the sequence data (including the accuracy of reads, quality scores for reads, and sequencingcoverage needs) has not yet been well d ...
Transposable element
A transposable element (TE or transposon) is a DNA sequence that can change its position within the genome, sometimes creating or reversing mutations and altering the cell's genome size. Transposition often results in duplication of the TE. Barbara McClintock's discovery of these jumping genes earned her a Nobel prize in 1983.TEs make up a large fraction of the C-value of eukaryotic cells. There are at least two classes of TEs: class I TEs generally function via reverse transcription, while class II TEs encode the protein transposase, which they require for insertion and excision, and some of these TEs also encode other proteins. It has been shown that TEs are important in genome function and evolution. In Oxytricha, which has a unique genetic system, they play a critical role in development. They are also very useful to researchers as a means to alter DNA inside a living organism.