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Topic: DNA sequences


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DNA

In the News (Thu 18 Apr 19)

  
  Significantly Lower Entropy Estimates for Natural DNA Sequences
DNA may be imagined to be a highly ordered, purposeful molecule, and one might therefore reasonably expect statistical models of its string representation to produce much lower entropy estimates.
DNA may be imagined to be a highly ordered, purposeful molecule, and one might therefore reasonably expect statistical models of its string representation to produce much lower entropy estimates, and confirm our intuition that it is far from random.
The DNA sequences were chosen to pass the following criteria: sufficient length to support this type of entropy estimation method, inclusion of a wide variety of species and sequence types to evaluate the generality of the method, and inclusion of sequences used to benchmark other published methods.
www.pnylab.com /pny/papers/cdna/cdna/cdna.html   (7298 words)

  
 Curved DNA in promoter sequences
Nair reported the presence of an intrinsic DNA bend with a broad locus of curvature for the human cdc2 promoter and concluded that this intrinsic bend might influence the protein-induced bending of a promoter region and therefore the subsequent interaction of regulatory factors with the transcription machinery [Nair, 1998].
Sequences of human exons and introns were taken from the Non-Redundant Functionally Equivalent Sequences Database (NRFES) of Konopka [Konopka, 1993].
Furthermore, recent studies on the sequence patterns in nucleosomal DNA indicates that only certain DNA sequences bind to the most stable nucleosome subset and that there is a significant amount of these sequences in centromeres suggesting a functional role for these stable nucleosomes [Widlund et al., 1997].
www.bioinfo.de /isb/1999/01/0017/main.html   (6238 words)

  
 DNA-Arrays.com: Information on DNA Arrays and DNA MicroArrays   (Site not responding. Last check: 2007-11-06)
The DNA sequences are bound to a surface such as a nylon membrane or glass slide at precisely defined locations on a grid.
DNA samples are prepared from the cells or tissues of interest.
Parameters such as the nucleotide content, the presence of secondary structure and the length of the DNA sequence on the array affect hybridization such that the signal intensity of the two species cannot be directly compared.
www.dna-arrays.com   (1279 words)

  
 Session 2: DNA sequences   (Site not responding. Last check: 2007-11-06)
DNA and RNA sequences are directly submitted from researchers and genome sequencing groups and collected from the scientific literature and patent applications.
Since the mid-1970s, the methods for isolating DNA sequences have been established and the understanding for the interpretation of genes was gained, the idea of mapping whole genomes was born.
It is possible to compare a nucleotide sequence against nucleotide databases (blastn), to compare a nucleotide sequence translated in all reading frames against protein sequence databases (blastx) and to compare the six-frame translations of a nucleotide sequence against the six-frame translations of a nucleotide sequence database (tblastx).
www.itb.uni-stuttgart.de /training/bioinformatics99/session_2.html   (2548 words)

  
 When Junk DNA Isn't Junk   (Site not responding. Last check: 2007-11-06)
One theory stated that non-coding DNA was "junk" that consisted of randomly-produced sequences that had lost their coding ability or partially duplicated genes that were non-functional.
The coding regions of DNA are concentrated in the chromosomal regions which are the richest in G (guanine) and C (cytosine) and seem to correspond to the telomeric regions of certain chromosome arms (T-bands) (8).
The roles of non-coding DNA are so numerous and pervasive that evolutionary studies are now looking at these sequences for patterns of "concerted evolution (71)." In summary, the non-coding DNA, contrary to statements by evolutionists, is not useless, but is, in fact, required for genomic functionality, therefore actually providing evidence of intelligent design.
www.godandscience.org /evolution/junkdna.html   (4292 words)

  
 Sequences, DNA & beyond glossary
Nucleic acid sequences are written with the 5' end to the left and the 3' end to the right, in reference to the direction of DNA synthesis during replication (from 5' to 3'), RNA synthesis during transcription (from 5' to 3'), and the reading of mRNA sequence (from 5' to 3') during translation.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA- dependent RNA polymerase during the initiation of transcription.
A sequence of DNA lying beyond the 3’ end of the coding segment of a gene which is recognized by RNA polymerase as a signal to stop synthesizing mRNA.
www.genomicglossaries.com /content/sequencing_dna_beyond_gloss.asp   (4620 words)

  
 DNA repeat sequences
Number of repeats may be unstable during DNA replication, e.g.
DNA replication may change repeat size in normals, but rarely out of usual range
Mutant (Large) repeat sequences not perfect: SCA 3 and Huntington's
www.neuro.wustl.edu /neuromuscular/mother/dnarep.htm   (736 words)

  
 DNA glossary
DNA, which consists of a polysugar- phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Sequences of DNA in the genes that are located between the EXONS.
www.genomicglossaries.com /content/DNA.asp   (2852 words)

  
 Incomplete nucleic acid sequences
Authors should always, however, make it clear which strand of DNA or RNA a given sequence refers to, and in circumstances where confusion between DNA and RNA is likely the sequence may be prefixed with the lower-case letter d or r, as in the previous recommendations [1].
Examples are given whereby the nomenclature is applied to sequences recognised by certain type II restriction endonucleases (Table 3) and to uncertainties in deriving a nucleic acid sequence from the corresponding amino acid sequence (Table 4).
For instance, the DNA of Escherichia coli is usually methylated on N-6 of the adenine residue in the sequence 5'-GATC-3' [23].
www.chem.qmul.ac.uk /iubmb/misc/naseq.html   (2915 words)

  
 DNA Music   (Site not responding. Last check: 2007-11-06)
The physio-musical conversion of DNA sequences occurs via a series of formulae that were worked out in a manner based on physical properties of DNA and musical parameters.
Once the sequences are converted by my custom algorithms and then played by the DNA Mixer, which reads linearly, much like the ribosomes—organelles that read codons for amino acid conversion—traverse the mRNA, and mixes multiple sequences just like in our cells.
The lengthy gene sequence of almost 1300 codons is played here as a five-part canon, much like it would be produced in our cells, that is, the reading of mRNA by ribosomes in multiple cells is not phase-locked—they do not all start reading their respective sequences at the same moment in time.
www.artic.edu /~pgena/DNAmus.html   (1268 words)

  
 DNA correlations: front page
DNA sequences carry biological information, DNA moleculars (double-stranded helix) obey physical laws, DNA genomes are products of generations of evolution, and DNA texts can be read as a string of symbols.
All these different aspects of DNA sequences (and to some extends, protein sequences) make their analysis a multi-disciplinary topic, which touches biochemistry, biophysics, evolutionary biology, as well as mathematics, statistics, computer science, and statistical physics.
In one sense, everything in biology has already been 'published' in the form of DNA sequences of genomes; but, of course, this is written in a language we do not yet understand.
www.nslij-genetics.org /dnacorr   (703 words)

  
 Biases in DNA sequences
As the replication mechanisms differ for the two strands of the DNA (continuous for one strand and discontinuous for the complementary strand), different mutational biases may produce different strand biases in terms of oligonucleotide distribution.
Furthermore, we have analyzed the sequences of the 5 genes before and after removal of DB (as in the experimental protocol of the papers).
These recognition sequences are symmetrical, comprising 4 to 8 specific base pairs, and cleavage and methylation occur symmetrically within the sequences.
abraxa.snv.jussieu.fr /research/thema/Biases   (2205 words)

  
 Characteristic Patch Sizes in DNA Sequences (ResearchIndex)   (Site not responding. Last check: 2007-11-06)
It is also known that the mosaic structure of DNA may affect the correlation properties of DNA sequences (Nee, 1992; Karlin and Brendel, 1993;Peng et al., 1994).
5 Characterizing long-range correlations in DNA sequences from..
5 Patchiness and correlations in DNA sequences (context) - Karlin, Brendel - 1993
citeseer.ist.psu.edu /207276.html   (409 words)

  
 DNA Informatics Corner   (Site not responding. Last check: 2007-11-06)
It is best to use the part(s) of the sequence that contain real DNA (good consensus regions) as the likelihood if these regions giving positive scores is higher than if they contained many 'N's which the programs will attempt to match to the entire database(s).
Sequence Retrieval System (version 5) is a World Wide Web interface for the recovery of nucleotide and protein sequences from a wide range of databases (list of more than 30 provided).
Sequence Analysis, Gene Assembly And Sequence Comparison Systems from the Informatics Group,Oak Ridge National Laboratory,Oak Ridge, Tennessee, U.S.A. is a suite of tools designed to provide analysis and putative annotation of DNA sequences both interactively and through the use of automated computation.
www.dur.ac.uk /biological.sciences/Bioinformatics/DNA_corner.htm   (3900 words)

  
 Clustering of DNA Sequences in Human Promoters -- FitzGerald et al. 14 (8): 1562 -- Genome Research
relative to the TSS, the DNA sequences that are in the cluster
is the Kozak sequence that clusters downstream of the TSS.
The number of occurrences of each 32,896 DNA sequence in the 13,010 promoter sequences is plotted as a gray dot.
www.genome.org /cgi/content/full/14/8/1562   (5996 words)

  
 CMGS-Interspersed repeats /23.9.97   (Site not responding. Last check: 2007-11-06)
An estimated third of human genome consists of interspersed repetitive DNA sequences which are primarily degenerate copies of transposable elements.
DNA Transposons Possess a single intron-less open reading frame encoding the transposase with Two short inverted repeat sequences flanking the reading frame (TIR).
Post-implantation development period when Genome is scanned for repetitive DNA sequences which are inactivated by DNA methylation.
www.ich.ucl.ac.uk /cmgs/line.htm   (517 words)

  
 HUGO Statement on the Patenting of DNA Sequences   (Site not responding. Last check: 2007-11-06)
An expressed sequence tag (EST) is part of a sequence from a cDNA clone that corresponds to an mRNA.[26] An EST can therefore be used to identify an expressed gene, and can also be used as a sequence-tagged site marker[11] to locate that gene on a physical map of the genome.
Determining function for a sequence is a matter of tremendous complexity, requiring biological experiments of the highest order of creativity.
In contrast to sequence analysis, the task of establishing actual biological functions requires specific experiments that are individually tailored to the particular gene.
www.gene.ucl.ac.uk /hugo/patent.htm   (2963 words)

  
 Divergence of DNA sequences   (Site not responding. Last check: 2007-11-06)
When the percent difference display is chosen, the vertical axis shows the percent difference between two sequences.
The blue dots show data simulated according to the chosen model of sequence evolution.
The red dots show data that falls outside the plot boundaries.
darwin.eeb.uconn.edu /simulations/dna-dist.html   (260 words)

  
 Genome Projects - The Institute for Genomic Research
TIGR's Genome Projects are a collection of curated databases containing DNA and protein sequence, gene expression, cellular role, protein family, and taxonomic data for microbes, plants and humans.
Containing the complete set of sequence reads, quality values, and ancillary data for selected genome projects, for use in comparing assemblers or polymorphism studies.
Integrating data from international EST sequencing and gene research projects, the Gene Indices are an analysis of the transcribed sequences represented in the world's public EST data.
www.tigr.org /tdb   (391 words)

  
 HUGO Statement on Patenting of DNA sequences   (Site not responding. Last check: 2007-11-06)
Notwithstanding its generally positive attitude toward patenting of useful benefits derived from genetic information, HUGO has repeatedly observed that Expressed Sequenced Tags (ESTs) constitute research tools and therefore opposed the patenting of short sequences from randomly isolated portions of genes and transcripts encoding proteins of uncertain functions.
Apart from this, the discovery of the importance of Single Nucleotide Polymorphisms (SNPs) for diagnostics and the attempts aimed at their patenting, led to the establishment of the non-profit SNP (TSC) Consortium of industry and academia.
emphasizes its basic understanding that DNA molecules and their sequences, be they full-length, genomic or cDNA, ESTs, SNPs or even whole genomes of pathogenic organisms, if of unknown function or utility, as a matter of policy, in principle, should be viewed as part of pre-competitive information.
www.gene.ucl.ac.uk /hugo/patent2000.html   (733 words)

  
 The Physical Map of Candida Albicans
The completion of the 10.7x sequence of the Candida albicans genome and its annotation has provided Candida researchers with important tools for the analysis of this important human pathogen.
However, since the sequence has not yet been finished and there is no genetic map, ordering and assignment to chromosomes of contigs and their genes cannot be accomplished without a physical map.
The translocations have all occurred at or near Major Repeat Sequences.
albicansmap.ahc.umn.edu   (467 words)

  
 DDBJ Homepage   (Site not responding. Last check: 2007-11-06)
DDBJ (DNA Data Bank of Japan) began DNA data bank activities in earnest in 1986 at the National Institute of Genetics (NIG).
DNA sequence records the organismic evolution more directly than other biological materials and,thus, is invaluable not only for research in life sciences, but also human welfare in general.
Release of transcript sequences derived from human and mouse with a huge scale(Oct.3)
www.ddbj.nig.ac.jp   (146 words)

  
 Immunostimulatory DNA Sequences   (Site not responding. Last check: 2007-11-06)
You may also be able to place a request for this book via these links: BN.com and Overstock.com
Book Description: This volume is a product of a collaborative effort and attempts to provide a wide and up-to-date coverage of information regarding the biology and on the potential application of immunostimulatory DNA.
ISS hold great promise for influencing the immune response and the authors anticipate that the high efficacy and low toxicity observed in animal models will translate into success in a variety of human clinical applications.
isbn.nu /3540677496   (322 words)

  
 ttaggg biologie
Telomeres are the ends of chromosomes and consist of short, tandemly repeated [(TTAGGG)n]> DNA sequences which are associated with various proteins.
Due to incomplete DNA replication, during S phase of each cell cylce, parts of these telomeres are lost.
Telomeric repeat (5' to 3' toward the end)
www.esculape.com /biologie/ttaggg.html   (343 words)

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