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*  Ancestral reconstruction
For example, PAML is a collection of programs for the phylogenetic analysis of DNA and protein sequence alignments by maximum ... These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the ... The Bayesian analysis of genetic sequences may confer greater robustness to model misspecification. MrBayes allows inference of ... Rather than inferring the ancestral DNA sequence, one may be interested in the larger-scale molecular structure and content of ...
*  Phylogenesis
... such as DNA sequences or overall morpho-anatomical, ethological, and other characteristics. The result of these analyses is a ... Phylogenetics is the branch of life science concerned with the analysis of molecular sequencing data to study evolutionary ... The outcome of a cladistic analysis is a cladogram - a tree-shaped diagram (dendrogram) that is interpreted to represent the ... Phylogenetic analyses have become central to understanding biodiversity, evolution, ecological genetics and genomes. Cladistics ...
*  Molecular phylogenetics
Typical molecular systematic analyses require the sequencing of around 1000 base pairs. At any location within such a sequence ... Sanger F, Coulson AR (May 1975). "A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase". J. ... These have been replaced in recent times largely by DNA sequencing, which produces the exact sequences of nucleotides or bases ... In the period of 1974-1986, DNA-DNA hybridization was the dominant technique. Every living organism contains DNA, RNA, and ...
*  Nested polymerase chain reaction
... via a temperature-mediated DNA polymerase. The products can be used for sequencing or analysis, and this process is a key part ... The target DNA undergoes the first run of polymerase chain reaction with the first set of primers, shown in green. The ... Conventional PCR requires primers complementary to the termini of the target DNA. The amount of product from the PCR increases ... A commonly occurring problem is primers binding to incorrect regions of the DNA, giving unexpected products. This problem ...
*  Molecular cloning
... restriction fragment analysis and/or DNA sequencing. Molecular cloning provides scientists with an essentially unlimited ... The desired products (vector DNA covalently linked to foreign DNA) will be present, but other sequences (e.g. foreign DNA ... vector DNA with no recombinant sequence inserted). In these vectors, foreign DNA is inserted into a sequence that encodes an ... if any segment of DNA from any organism is inserted into a DNA segment containing the molecular sequences required for DNA ...
*  Borrelia lusitaniae
by 16S Ribosomal DNA Sequence Analysis". International Journal of Systematic Bacteriology. 47 (4): 921-925. doi:10.1099/ ... Molecular analysis of the patient isolate allowed the classification of the strain to B. lusitaniae, a genospecies previously ... Vitorino, L. L.; Margos, G.; Zé-Zé, L.; Kurtenbach, K.; Collares-Pereira n, M. (2010). "Plasmid profile analysis of Portuguese ... "Fine-Scale Phylogeographic Structure of Borrelia lusitaniae Revealed by Multilocus Sequence Typing". PLoS ONE. 3 (12): 1-13. ...
*  Molecular Biology Core Facilities
DNA sequencing Massively Parallel Sequencing "next-gen sequencing" Full genome sequencing Gene mapping SNP analysis Genotyping ... We have developed a method for the partial automation of DNA sequence analysis. Fluorescence detection of the DNA fragments is ... synthesis of fluorescent DNA primers for use in DNA sequence analysis. Note that Oxford University Press, the publishers of the ... 1986 Jun 12-18;321(6071):674-9. Fluorescence detection in automated DNA sequence analysis. ...
*  Droplet-based microfluidics
"DNA sequence analysis with droplet-based microfluidics". Lab on a Chip. 13 (24): 4864. doi:10.1039/c3lc50905b. Shendure, Jay; ... cost-effective approach to DNA sequencing that provides high throughput and high accuracy sequencing information. DNA ... Commercially available devices utilizing cyclic-array sequencing of DNA, and tag sequences with intermediate fluorophore ... DNA sequence information gathered from healthy and diseased tissues is highly valuable in the medical field as mutations can be ...
*  Nigrospora sphaerica
DNA sequence analysis further confirmed the identity. Another case found N. sphaerica isolated from a corneal ulcer. A woman in ... rRNA sequence comparison of the ITS region confirmed N. sphaerica identity. Cases of leaf spot disease of kiwi fruit (Actinidia ... Analysis of corneal scrapings showed presence of hyphae elements suggesting cause of ulcer from a fungal pathogen. Isolated ...
*  Euarchonta
1999b). Further DNA sequence analyses (Madsen et al. 2001, Murphy et al., 2001 Waddell et al. 2001) supported the Euarchonta ... Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet. 3:e2, doi:10.1371/journal. ... 2001) showing near total congruence of mtDNA-based and nuclear-based trees when such sequences were excluded, some authors ... Kumar, Vikas; Hallström, Björn M.; Janke, Axel (2013-04-01). "Coalescent-Based Genome Analyses Resolve the Early Branches of ...
*  Genetic variability
Kunz BA, Ramachandran K, Vonarx EJ (April 1998). "DNA sequence analysis of spontaneous mutagenesis in Saccharomyces cerevisiae ... Most DNA damages are accurately repaired by various DNA repair mechanisms. However, some DNA damages remain and give rise to ... that is often employed in repair of DNA double-strand breaks. (Also see Mutation.) Thus it seems that DNA damages are the ... DNA damages are very frequent, occurring on average more than 60,000 times a day per cell in humans due to metabolic or ...
*  Barolo shearwater
Mitochondrial DNA cytochrome b sequence analysis (Austin et al., 2004) indicates, however, that baroli and boydi are very close ...
*  Oligonucleotide synthesis
"Light-generated oligonucleotide arrays for rapid DNA sequence analysis". Proc. Natl. Acad. Sci. U.S.A. 91 (11): 5022-5026. ... primers for DNA sequencing and amplification, probes for detecting complementary DNA or RNA via molecular hybridization, tools ... "QMaster DNA/RNA Synthesizer". Genomictechnologies.com. "QMaster DNA/RNA Synthesizer". www.genomictechnologies.com/QmasterII. ... "DNA / RNA Oligonucleotide Synthesizer: MerMade". Bioautomation.com. Retrieved 2011-10-18. "Azco DNA/RNA Synthesizers". ...
*  Lithuania
Dalia Kasperavičiūtė and Vaidutis Kučinskas (2004). "Mitochondrial DNA Sequence Analysis in the Lithuanian Population" (PDF). ... technology that allows insertion of new genes into the DNA or the correction of DNA errors. Softneta is famous for developing ... A 2004 analysis of MtDNA in the Lithuanian population revealed that Lithuanians are close to the Slavic and Finno-Ugric ... An analysis revealed that roads are not sufficiently maintained and their condition is deteriorating compared to previous years ...
*  Arsenite-transporting ATPase
Arsenite-Antimonite efflux Silver S, Misra TK, Laddaga RA (1989). "DNA sequence analysis of bacterial toxic heavy metal ... Rosen BP, Weigel U, Monticello RA, Edwards BP (1991). "Molecular analysis of an anion pump: purification of the ArsC protein". ... Rosen BP, Weigel U, Monticello RA, Edwards BP (1991). "Molecular analysis of an anion pump: purification of the ArsC protein". ... "Crystallization and preliminary x-ray analysis of the catalytic subunit of the ATP-dependent arsenite pump encoded by the ...
*  Russian tortoise
DNA sequence analysis generally concurs, but not too robustly so. Some sources also list three separate subspecies of Russian ...
*  Stagnicola palustris
Bargues M. D., Artigas P., Jackiewicz M., Pointier J. P. & Mas-Coma S. (2005). "Ribosomal DNA ITS-1 sequence analysis of ... based on nuclear ribosomal DNA ITS-2 sequences". Infection, Genetics and Evolution 1: 85-107. ...
*  TAF7
"Comparative DNA sequence analysis of mouse and human protocadherin gene clusters". Genome Research. 11 (3): 389-404. doi: ... Cross SH, Charlton JA, Nan X, Bird AP (March 1994). "Purification of CpG islands using a methylated DNA binding column". Nature ...
*  PCDHB16
"Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters". Genome Res. 11 (3): 389-404. doi:10.1101/gr. ... The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 7 (4): 273-81. doi: ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... Nollet F, Kools P, van Roy F (2000). "Phylogenetic analysis of the cadherin superfamily allows identification of six major ...
*  Euphorbia
... few of the subgeneric circumscriptions hold up under DNA sequence analysis. According to a 2002 publication on studies of DNA ... is consistent with nuclear and chloroplast DNA sequence data in testing of about 10% of its members. This testing supports ... The genus may be described by properties of its members' gene sequences, or by the shape and form (morphology) of its heads of ... in southern Africa based on ITS and psbA-trnH sequence data". Taxon. 55 (2): 397-420. doi:10.2307/25065587. Steinmann, Víctor W ...
*  PCDHB4
2001). "Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters". Genome Res. 11 (3): 389-404. doi: ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... Nollet F, Kools P, van Roy F (2000). "Phylogenetic analysis of the cadherin superfamily allows identification of six major ...
*  PCDHGA11
2001). "Comparative DNA sequence analysis of mouse and human protocadherin gene clusters". Genome Res. 11 (3): 389-404. doi: ... 2000). "Shotgun sequencing of the human transcriptome with ORF expressed sequence tags". Proc. Natl. Acad. Sci. U.S.A. 97 (7): ... "Entrez Gene: PCDHGA11 protocadherin gamma subfamily A, 11". Nollet F, Kools P, van Roy F (2000). "Phylogenetic analysis of the ... "Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence" (PDF). ...
*  PCDHB15
2001). "Comparative DNA sequence analysis of mouse and human protocadherin gene clusters". Genome Res. 11 (3): 389-404. doi: ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... "Entrez Gene: PCDHB15 protocadherin beta 15". Nollet F, Kools P, van Roy F (2000). "Phylogenetic analysis of the cadherin ...
*  PCDHA4
2001). "Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters". Genome Res. 11 (3): 389-404. doi: ... 2004). "The DNA sequence and comparative analysis of human chromosome 5". Nature. 431 (7006): 268-74. doi:10.1038/nature02919. ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... Nollet F, Kools P, van Roy F (2000). "Phylogenetic analysis of the cadherin superfamily allows identification of six major ...
*  PCDH10
2001). "Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters". Genome Res. 11 (3): 389-404. doi: ... The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 7 (1): 65-73. doi: ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... Cross SH, Charlton JA, Nan X, Bird AP (1994). "Purification of CpG islands using a methylated DNA binding column". Nat. Genet. ...
*  UCKL1
2002). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 (6866): 865-71. doi:10.1038/414865a. ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... 2006). "A probability-based approach for high-throughput protein phosphorylation analysis and site localization". Nat. ...
*  PCDHGA12
2001). "Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters". Genome Res. 11 (3): 389-404. doi: ... The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro". DNA Res. 5 (1): 31-9. doi ... "Entrez Gene: PCDHGA12 protocadherin gamma subfamily A, 12". Nollet F, Kools P, van Roy F (2000). "Phylogenetic analysis of the ... 1998). "Prediction of the coding sequences of unidentified human genes. IX. ...