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*  Ancestral reconstruction
The Bayesian analysis of genetic sequences may confer greater robustness to model misspecification. MrBayes allows inference of ... These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the ... For example, PAML is a collection of programs for the phylogenetic analysis of DNA and protein sequence alignments by maximum ... HyPhy, Mesquite, and MEGA are also software packages for the phylogenetic analysis of sequence data, but are designed to be ...
*  Phylogenesis
Phylogenetics is the branch of life science concerned with the analysis of molecular sequencing data to study evolutionary ... such as DNA sequences or overall morpho-anatomical, ethological, and other characteristics. The result of these analyses is a ... 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 ... Modern sequence comparison techniques overcome this objection by the use of multiple sequences. Once the divergences between ... These have been replaced in recent times largely by DNA sequencing, which produces the exact sequences of nucleotides or bases ... Bast, F. (2013). "Sequence Similarity Search, Multiple Sequence Alignment, Model Selection, Distance Matrix and Phylogeny ...
*  Nested polymerase chain reaction
The products can be used for sequencing or analysis, and this process is a key part of many genetics research laboratories, ... only one containing the intended sequence. The product from the first reaction undergoes a second run with the second set of ... and alternative primer target sequences. Books at your local library about nested polymerase chain reactions Scholarly articles ...
*  Molecular cloning
... restriction fragment analysis and/or DNA sequencing. Molecular cloning provides scientists with an essentially unlimited ... The idea arose that different DNA sequences could be inserted into a plasmid and that these foreign sequences would be carried ... vector DNA with no recombinant sequence inserted). In these vectors, foreign DNA is inserted into a sequence that encodes an ... Virtually any DNA sequence can be cloned and amplified, but there are some factors that might limit the success of the process ...
*  Sequence analysis
According to Michael Levitt, sequence analysis was born in the period from 1969-1977. In 1969 the analysis of sequences of ... Pair-wise sequence alignment only compares two sequences at a time and multiple sequence alignment compares many sequences. Two ... Machine Clustering Bayesian Network Regression Analysis Sequence mining Alignment-free sequence analysis List of sequence ... In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of ...
*  Social sequence analysis
... is a special application of sequence analysis, a set of methods that were originally designed in ... "Sequence Analysis: New Methods for Old Ideas." Annual Review of Sociology 21:93-113. Abbott, Andrew. 1995. "Sequence Analysis: ... Brendan Halpin's sequence analysis page at the University of Limerick. Laurent Lesnard's Stata plugin for sequence analysis ... of sequence analysis. Scholars who have made important contributions to social sequence analysis theory, techniques, data ...
*  Bowtie (sequence analysis)
Bowtie is a software package commonly used for sequence alignment and sequence analysis in bioinformatics..The source code for ... The Bowtie sequence aligner was originally developed by Ben Langmead et al. at the University of Maryland in 2009. The aligner ... Bowtie is promoted as "an ultrafast, memory-efficient short aligner for short DNA sequences." The speed increase of Bowtie is ... Bowtie is used as a sequence aligner by a number of other related bioinformatics algorithms, including TopHat, Cufflinks and ...
*  Alignment-free sequence analysis
The process has been applied to DNA sequence analysis. The use of iterated maps for sequence analysis was first introduced by ... Sequence analysis Multiple sequence alignment Phylogenomics Bioinformatics Metagenomics Next-generation sequencing Population ... The pioneering approaches for sequence analysis were based on sequence alignment either global or local, pairwise or multiple ... In bioinformatics, alignment-free sequence analysis approaches to molecular sequence and structure data provide alternatives ...
*  Targeted analysis sequencing
... (sometimes called target amplicon sequencing) (TAS) is a next-generation DNA sequencing technique ... Next-gen sequencing use shorter reads 50-400 base pairs which allow for quicker sequencing of multiple specimens. Thus TAS ... "Targeted DNA Methylation Analysis by Next-generation Sequencing". Journal of Visualized Experiments. 96: 52488. doi:10.3791/ ... Bybee, Seth M.; Bracken-Grissom, Heather (13 October 2011). et al.. "Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen ...
*  Cognitive analytic therapy
Bakhtin provided concepts such as dialogism from which come techniques such as Dialogical Sequence Analysis. This is a ... Original works published in 1934, 1960). Leiman, M. (2004). Dialogical sequence analysis. In: H. J. M. Hermans & G. Dimaggio ( ... A review of CAT looking back over the 30 years to its beginnings contains a meta-analysis of 11 outcome studies of CAT. The ... In addition to the procedural sequence model, a second distinguishing feature of CAT is the use of reciprocal roles (RRs). ...
*  Dialogical self
On the basis of Mikhail Bakhtin's theory of utterances, Leiman devised a dialogical sequence analysis. This method starts from ... Leiman, M. (2004). Dialogical sequence analysis. In: H. J. M. Hermans & G. Dimaggio (eds.), The dialogical self in ... On the basis of the results of the quantitative analysis, some positions can be selected, by the client or assessor, for closer ... The simplest approach, however, is to perform a standard principal component analysis (PCA). To obtain a bi-plot, a PCA is once ...
*  GYPB
Purification and sequence analysis". J. Biol. Chem. 262 (12): 5808-11. PMID 3571235. Dahr W, Beyreuther K, Moulds J, Unger P ( ... It was first sequenced in 1987 the peptide sequence of 72 amino acids having been determined earlier that year. The gene has 97 ... The transition site from homologous to nonhomologous sequences can be localized within Alu repeat sequences. There are ~80000 ... There is a signal sequence of 19 amino acid residues. The leader peptide differs by one amino acid and the next 26 amino acids ...
*  Spot 42 RNA
I. Nucleotide sequence analysis". J. Mol. Biol. 131 (3): 573-92. doi:10.1016/0022-2836(79)90008-1. PMID 390161. Ikemura, ... In E. coli the spf gene is flanked by polA (upstream) and yihA (downstream). A CRP binding sequence and -10 and -35 promoter ... Bækkedal and Haugen made a Spot42 consensus secondary structure based on all known "spf" sequences at the time (2015) and found ... Beisel and Storz demonstrated with microarray analysis and reporter fusions that Spot 42 plays a broader role in metabolism by ...
*  Tetratricopeptide repeat protein 39B
"NetPhos 2.0 Server". Center for Biological Sequence Analysis. Retrieved 13 May 2013. "SUMOsp 2.0 - SUMOylation Site Prediction ... According to an analysis of the secondary protein structure, TTC39B is most likely to be expressed in the endoplasmic reticulum ...
*  Transmembrane protein 217
Center for Biological Sequence Analysis. Miao, Y.; Cui, L.; Chen, Z.; Zhang, L (2016). "Gene expression profiling of DMU-212- ... "Methods and algorithms for statistical analysis of protein sequences". Proceedings of the National Academy of Sciences. 89: ... Co-expression analyses have found that TMEM217 was up-regulated in response to mechanical stretch in dermal fibroblast cells ... No known function has been attributed to TMEM217, however a co-expression analysis in dermal fibroblasts has predicted the ...
*  C9orf84
"NetOGlyc". Center for Biological Sequence Analysis. "NetNES". Center for Biological Sequence Analysis. "SAPS". SDSC Biology ... The primarily used sequence in humans is C9orf84 Isoform 1. This isoform is 1444 aa long, contains 26 exons, has a predicted ... C9orf84 is the only gene in the human genome with its particular sequence. This gene is found in all vertebrates, and some ... "A comprehensive functional analysis of tissue specificity of human gene expression". BMC Biology. 6: 49. doi:10.1186/1741-7007- ...
*  Transmembrane protein 251
Center of Biological Sequence Analysis. Retrieved 9 May 2015. "NetPhosK 1.0 Server". NetPhosK 1.0 Server. Center of Biological ... Sequence Analysis. Retrieved 9 May 2015. "NetAcet 1.0 Server". NetAcet 1.0 Server. Center of Biological Sequence Analysis. ... TMEM251 has a multitude of mutations in its 5'UTR, coding sequence, and 3'UTR. The majority of the mutations observed are ... Both consists of two exons that include the entire coding sequence for the TMEM251 protein. Figure 1: Chromosome 14 overview. ...
*  TopHat (bioinformatics)
TopHat is a bioinformatic sequence analysis package tool for fast and high throughput alignment of shotgun cDNA sequencing ... Bowtie (sequence analysis) Trapnell, C.; Pachter, L.; Salzberg, S. L. (16 March 2009). "TopHat: discovering splice junctions ...
*  Magnus Manske
2012). "Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing". Nature. 487 (7407): 375-9. doi: ... Magnus Manske on Twitter Alastair Kerr (21 June 2011). "Desktop Sequence Analysis: software review". Bioinformatics Knowledge ... Manske, H. M.; Kwiatkowski, D. P. (2009). "Look Seq: A browser-based viewer for deep sequencing data". Genome Research. 19 (11 ... which minimizes errors in sequencing. As a student, Manske was one of the most active contributors to the Nupedia project, ...
*  Transfer-messenger RNA
Comparative sequence analysis indicates features typical for mt-tmRNAs. Most conserved is the primary sequence of the amino ... Zwieb C, Wower I, Wower J (1999). "Comparative sequence analysis of tmRNA". Nucleic Acids Res. 27 (10): 2063-71. doi:10.1093/ ... The complete E. coli tmRNA secondary structure was elucidated by comparative sequence analysis and structural probing. Watson- ... Eddy, S.; Durbin, R. (1994). "RNA sequence analysis using covariance models". Nucleic Acids Res. 22 (11): 2079-2088. doi: ...
*  Jürgen Brosius
Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 1993 Nov ... Protein sequence analysis: automated microsequencing. Science. 1983 Feb 11;219(4585):650-9. Brosius J, Dull TJ, Sleeter DD, ... There, he sequenced the first large ribosomal RNAs via their genes utilizing the Maxam-Gilbert sequencing method. It took ~2.5 ... Some of his scientific contributions involve the first genetic sequencing of a ribosomal RNA operon, the design of plasmids for ...
*  C3orf14
Combet C, Blanchet C, Geourjon C, Deléage G (March 2000). "NPS@: network protein sequence analysis". Trends in Biochemical ... Pruitt KD, Tatusova T & Maglott DR (January 2007). "NCBI reference sequences (RefSeq): a curated non-redundant sequence ... Transcripts have not been identified in amphibians or insects; however only model organisms have been sequenced from these ... Bilofsky, Howard; Burks, Christian (11 March 1988). "The GenBank® genetic sequence data bank". Nucleic Acids Research. 16 (5): ...
*  Band-pass filter
Atomic line filter Audio crossover Band-stop filter E. R. Kanasewich (1981). Time Sequence Analysis in Geophysics. University ... Band-pass filters can help with finding where stars lie on the main sequence, identifying redshifts, and many other ...
*  List of RNA structure prediction software
Eddy SR, Durbin R (1994). "RNA sequence analysis using covariance models". Nucleic Acids Res. 22 (11): 2079-88. doi:10.1093/nar ... Bauer M, Klau GW, Reinert K (2007). "Accurate multiple sequence-structure alignment of RNA sequences using combinatorial ... "Noncoding RNA gene detection using comparative sequence analysis". BMC Bioinformatics. 2 (1): 8. doi:10.1186/1471-2105-2-8. PMC ... a multiple sequence alignment editor and analysis workbench". Bioinformatics. 25 (9): 1189-91. doi:10.1093/bioinformatics/ ...
*  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. ...
*  Richard Perham
Instrumentation in amino acid sequence analysis. London New York: Academic Press. ISBN 9780125512503. Perham, Richard N; ... Instrumentation in amino acid sequence analysis. London New York: Academic Press. ISBN 9780125512503. Scrutton, Nigel Shaun ( ...