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Topic: GC-content

    Note: these results are not from the primary (high quality) database.

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GC - Transition to College Courses Except in mathematics, students saw the content of GC courses as different from high school courses in the same area. GC students were split in their assessment of the difficulty of GC courses compared to their high school courses. GC instructors were asked to distribute the surveys in their courses during the last week of the quarter as a part of a routine course evaluation. www.gen.umn.edu /research/ore/reports/coll_transition.html

Cis-acting modifiers of expanded CAG/CTG triplet repeat expandability: associations with flanking GC content and proximity to CpG islands -- Brock et al. 8 (6): 1061 -- Human Molecular Genetics GC content has been shown previously to affect the conformational properties of DNA( 30), and it is possible that flanking DNA structures modify repeat metabolism. Interestingly, although the flanking GC content of the most unstable repeat, DM, is not as high as that of some of the other loci, it is located in a very large (~3 kb) unmethylated CGI ( 33). It is possible that GC content and relative mutabilities of repeat sequences are both responding to some higher order effect of genomic organization, such as location within different isochore subtypes ( 28). hmg.oupjournals.org /cgi/content/full/8/6/1061

Figure 36 For exons and introns, the local GC content was derived from alignments to finished sequence only, and were calculated from windows covering the feature or 10,000 bp centred on the feature, whichever was larger. GC content for the genome was calculated for adjacent nonoverlapping 20,000-bp windows across the sequence. For 9,315 known genes mapped to the draft genome sequence, the local GC content was calculated in a window covering either the whole alignment or 20,000 bp centred around the midpoint of the alignment, whichever was larger. www.nature.com /nature/journal/v409/n6822/fig_tab/409860a0_F36_lgnd.html

The Graph Menus This is similar to the GC content graph, but the plot is clipped so that the GC content of each algorithm window is shown only when it is more than 2.5 times the standard deviation of the GC content in all the windows. This is a graph of the average GC content of a moving window (default size 120 base), across the bases visible in the overview window. This graph is similar to the GC content graph but shows the GC content of the first, second and third position independently. www.genomics.purdue.edu /gcg/act/x257.htm

Homology-dependent methylation in primate repetitive DNA -- Meunier et al. 102 (15): 5471 Data Supplement - HTML Page - index.htslp -- Proceedings of the National Academy of Sciences The regional GC content relative to a CpG site was defined as the GC content in a 100-kb window centered on the site. Variations in substitution patterns may be influenced by regional factors such as GC content or recombination rate (1, 2). CpG substitution rate in nonrepetitive DNA as a function of regional GC content. www.pnas.org /cgi/content/full/0408986102/DC1

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Identification and prevention of a GC content bias in SAGE libraries -- Margulies et al. 29 (12): 60 -- Nucleic Acids Research Whereas, the similar slopes between Amp1 and Amp5 for both the 10 and 50% GC-rich SAGE Tag suggests that there is no bias with respect to GC content of a SAGE Tag in Amp5. GC content of the SAGE Tags in a library. Here, the distribution of V is similarly distributed for all percentages of GC content. nar.oupjournals.org /cgi/content/full/29/12/e60

Encyclopedia: GC-content The GC content can be measured by several means but one of the simplest methods is to measure what is called the melting temperature of the DNA double helix with a spectrophotometer. In genetics, the guanine-cytosine content (GC content) is the ratio of guanine and cytosine to the total number of nucleotides of a given genome. It is used, among other things, to easily distinguish between different species when a doubt remains. www.nationmaster.com /encyclopedia/GC_content

Plasmodium falciparum Chromosome 1 The color of the bars correlates to the local deviation from the mean GC content. Regions with mean GC content are blue and regions highest deviations are red. The X-axis corresponds to base positions and is centered at the mean GC content. izblapaz.unibe.ch /cgi-bin/old/gc.cgi?chr=1&org=Plasmodium_falciparum

Genome Biology Full text A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes We have shown that the GC content of individual codons and amino acids is the primary determinant of their response to biases in sequence composition, both among and (to a lesser extent) within genomes. The relationship between GC content and codon and amino-acid usage is ahistorical; it is replicated independently in the three domains of living organisms, reinforcing the idea that genes and genomes at mutation/selection equilibrium reproduce a unique relationship between nucleic acid and protein composition. If distantly related species with similar GC contents have the same amino-acid or codon usages, we can conclude that phylogenetic constraints are relatively unimportant, and perhaps that genomes are at or near equilibrium with respect to mutation and selection (otherwise, different unrelated species would not attain the same amino-acid composition predicted from the nucleotide composition). genomebiology.com /2001/2/4/research/0010

Chromatiaceae The GC content of the DNA is 64 -65 mol%. The GC content of the DNA is 61-68 mol%. The GC content of the DNA is 63-70 mol%. www.microbionet.com.au /chromatiaceae.htm

RNA Designer - Help In cases, where many sequences exist for a given structure (or substructure), the output sequences can be expected to match the specified target GC content quite closely; in cases where finding a correctly folding sequence with the target GC content is hard or impossible, the search is allowed to drift from the GC target. This may vary from the specified target GC content values, particularly in cases where there are few sequences that are predicted into the desired structure. These parameters can be used to control the target GC content of paired / unpaired bases in the desired structure, and are specified as percentages. www.rnasoft.ca /rnadesign_help.html

TDPRI :: View topic - What are they thinking?!?!? (GC content) About 10 yrs ago I went to GC to buy a DRRI, I was playing in a "classic RandR" band that played a lot of CCR, so I semi-crank this DR turn on the tremelo and play a couple minutes of "Born on the Bayou" and probably 5 other CCR bits. GC still uses ie and one look at some of the feedback ratings will show that a lot of people are ticked. I stopped going there 6 months ago when I got tired of the savagely poor condition of their Les Pauls, pushy sales guys pulling the old "the guitar case is extra" crap and prices that lead me to suspect they don't think anyone has a computer and access to great on line dealers. www.tdpri.com /viewtopic.php?t=28445&sid=cd97ee69800a297842ffb1b6d01ad228

Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution -- Hardison et al. 13 (1): 13 -- Genome Research Fullerton, S.M., Carvalho, A.B., and Clark, A.G. Local rates of recombination are positively correlated with GC content in the human genome. Hurst, L.D. and Willliams, E.J.B. Covariation of GC content and the silent site substitution rate in rodents: Implications for methodology and for the evolution of isochores. Pairwise correlations for various divergence measures, before and after correcting for the effect of GC content, difference in GC content between human and mouse, and CpG density in human. www.genome.org /cgi/content/full/13/1/13?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1066338658153_1552&stored_search=&FIRSTINDEX=0&volume=13&firstpage=13&journalcode=genome

Evaluating the Usefulness of Stem-loop Characteristics in Pinpointing Structural RNA Genes Problematic however is the rising tide of GC content in the counterparts to structural RNA’s as we move across the GC spectrum from AT rich to GC rich organisms. Having assembled this data, our task is to determine whether or not a stem-loop metric or combination of stem-loop related metrics sufficiently correlates with the presence of structural RNA genes along genomic sequences across the entire GC content spectrum. However, as we study organisms with increasing GC content the average distance between stem-loops in structural RNA’s and its genomic counterparts begins to merge. www.iscb.org /ismb2004/posters/kirtnoelATsfu.ca_641.html

A Unique Set of 11,008 Onion Expressed Sequence Tags Reveals Expressed Sequence and Genomic Differences between the Monocot Orders Asparagales and Poales -- Kuhl et al. 16 (1): 114 -- THE PLANT CELL Mean GC Content as a Function of Position (5' to 3') across 129-bp Sliding Windows for 279 Homologous Full-Length Sequences of Arabidopsis, Onion, and Rice. Distribution of GC Content for Large EST Data Sets of Arabidopsis, Onion, and Rice. GC Percentage Plots from 279 Homologous Full-Length Coding Regions of Arabidopsis versus Onion and Rice for the Entire Coding Region and for the First, Second, and Third Codon Positions. www.plantcell.org /cgi/content/full/16/1/114

Figure 13 The GC content in subregions of a 100-Mb region of chromosome 1 is plotted, starting at about 83 Mb from the beginning of the draft genome sequence. Middle, GC content of the first 10 Mb, analysed in 2-kb windows. Bottom, GC content of the first 1 Mb, analysed in 200-bp windows. www.nature.com /nature/journal/v409/n6822/fig_tab/409860a0_F13.html

Insertion site preferences of the P transposable element in Drosophila melanogaster -- Liao et al. 97 (7): 3347 -- Proceedings of the National Academy of Sciences In the profile of GC content, the heavy line represents actual EP insertion sites whereas the light line represents the same number of randomly picked 500-bp genomic sequences. GC content was then calculated for a 500-bp segment of genomic DNA centered on the P element insertion site using a window Profiles of GC content and the four indicated DNA physical measures in 500-bp segments of DNA derived from 467 independent, aligned P insertion sites. www.pnas.org /cgi/content/full/97/7/3347

Bioinformatics Since GC bonds confer greater stability on nucleic acid secondary structure than AT bonds, their data strongly suggest that an increase of G + C content is needed for the stabilization at high temperature of rRNA secondary structure (stem-loops), but not of DNA secondary structures. If one compares the distribution of DNA molecules of Tetrahymena strains of different mean GC contents, it is clear that the difference in mean values is due to a rather uniform difference of GC content in individual molecules. The relative molar content of each amino acid is expressed as a percentage of the amino acid content over the sum of stable amino acids: 1ysine, histidine, arginine, aspartic acid plus asparagine, glutamic acid plus glutamine, proline, alanine, valine, leucine, tyrosine, and phenylalanine. post.queensu.ca /~forsdyke/bioinfor.htm

GC-content - Wikipedia, the free encyclopedia In genetics, GC-content ( guanine-cytosine content) is a characteristic of the It is the proportion of GC- base pairs in the en.wikipedia.org /wiki/GC-content

BioMed Central Full text Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays The GC content of a Pinus species genome is about 40%, which is considerably closer to the 48% GC content of T7 phage (or the 50% GC content of Escherichia coli, the typical host of T7 phage), than for the 67% GC content of Thermus aquaticus [ 18-20 ]. Comparison of the selected genes (309 ESTs) differentially represented in the two amplification methods, the GC content of the ESTs, contigs and Arabidopsis thaliana cDNAs (on a nucleotide level) there was a significantly greater mean GC content for the sequences of the S' group than for those of the M' group. This might be reflected in the GC content and the temperature environment of the original organism for each polymerase. www.biomedcentral.com /1471-2164/6/61

PROMOTERS: AT/GC CONTENT AND PROPERTIES OF TATA BOX Such islands, nonmethylated DNA regions with a higher content of CpG dinucleotides relative to the remainder of the genome, are typical of vertebrate genes [7]. Characteristic of these DNA islands is the length of over 200 nucleotides, over 50% G+C content, and the ratio of observed/expected (Obs./Exp.) CpG dinucleotides >0.6. High expressed genes including housekeeping genes as well as certain genes with limited or tissue-specific expression are known to be associated with CpG islands starting in the 5' region relative to the TSS. dragon.bionet.nsc.ru /bgrs/thesis/32/index.html

Genome Biology Full text Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana Rates of crossing over have been shown to correlate not only with the GC content of synonymous sites, where weak natural selection is expected to act on codon-usage bias, but also with the GC content of noncoding sites [ 6, 22 ]. The expected change in GC content due to BGC in the case of inbreeding can be derived straightforwardly from population genetics theory (see Materials and methods for details). Both the GC content at synonymous sites and at introns are likely to be influenced by genetic drift [ 49 ]. www.genomebiology.com /2004/5/7/R45

04.Comparative Genomics If you encounter a DNA stretch in which the GC content is notoriously different than in neighbor sequences, you assume that this region has not evolved with the rest of the genome and that it arrived from a horizontal transfer. This is a curious aspect of evolution, the genome adjust to a particular GC content and this seems to be related with regulation of processes such as replication, transcription and so on. As I understand from the lecture (please refer slide 15), this plasticity zone are the part of the genome that horizontal gene transfer could take place(as suggested), that signify by the difference in GC content (genes from non-h pylori) and led to strain specific genetic diversity among H pylori isolates/species. www.sanbi.ac.za /FAQ/list2/4.htm

GC content The GC content web server allows users to have from a query sequences a.dat file that must be cut and paste in a text file then can be loaded in a spreadsheet (EXCELL work very nice) or something else, to see graphically the profile of GC content. where the 1st col. indicate the bp (one hundred to one hundred), the 2nd indicate the percentage in GC, 3th show the CpG island. This file loaded in EXCELL will give you a graphic that will contain, on abscisses total lenght in bp, in ordinates the % of GC; moreover if present, the graphic will show the CpG island. 140.164.7.8 /grsl/cgconten.html

Abnormal DNA methylation and deoxycytosine-deoxyguanine content in nucleosomes from lymphocytes undergoing apoptosis -- HUCK et al. 13 (11): 1415 -- The FASEB Journal Sano, H., Morimoto, C. (1982) DNA isolated from DNA/anti-DNA antibody immune complexes in systemic lupus erythematosus is rich in guanine-cytosine content. Corvetta, A., Della Bitta, R., Luchetti, M. M., Pomponio, G. (1991) 5-Methylcytosine content of DNA in blood, synovial mononuclear cells and synovial tissue from patients affected by autoimmune rheumatic diseases. Abnormal DNA methylation and deoxycytosine-deoxyguanine content in nucleosomes from lymphocytes undergoing apoptosis www.fasebj.org /cgi/content/full/13/11/1415

BioLinux: Bioinformatics and Linux course (2004) The point of this exercise is that (in bacteria) the coding regions there is a GC bias: the GC content of the first codon position is different from the second and third codon position. should compute the GC content for frame 2, that is, for the subsequence consisting of positions 1, 4, 7, 10, and so on. should compute the GC content specifically for frame 1, that is, for the subsequence consisting of positions 0, 3, 6, 9, and so on. www.bioinf.kvl.dk /biolinux/week5.html

CiteULike: GC/AT-content spikes as genomic punctuation marks. In vertebrates, sharp positive and negative spikes of GC content are observed at the transcription start and stop sites, respectively, and there is also a progressive decrease in GC content from the 5' untranslated region to the 3' untranslated region along the gene. In invertebrates, the positive and negative GC-content spikes at the transcription start and stop sites are preceded by spikes of opposite value, and the highest GC content is found in the coding regions of the genes. Sharp changes in GC content are detected at the transcription boundaries for all species analyzed, including human, mouse, rat, chicken, fruit fly, and worm. www.citeulike.org /user/LeightonP/article/3108

Assignment5.doc Finally, call the subroutine Max_Array (discussed in class) to determine the maximum GC content, and the index (between 0 to 19) of the string with this maximum content. Compute the GC content (as a percentage) of these 20 random strings by calling a subroutine named GC_Content for each one. In the event of a tie, take the first occurrence of the maximum GC content. gcat.davidson.edu /bioinformatics/assign_04/Assignment5.doc

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