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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 ... sequence of proteins by Frederick Sanger in 1955, Zuckerkandl and Pauling postulated that such sequences could be used to infer ... not only the phylogeny relating the observed protein sequences, but also the ancestral protein sequence at the earliest point ( ...
*  Molecular phylogenetics
Typical molecular systematic analyses require the sequencing of around 1000 base pairs. At any location within such a sequence ... Every living organism contains DNA, RNA, and proteins. In general, closely related organisms have a high degree of agreement in ... 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 ...
*  Molecular cloning
... restriction fragment analysis and/or DNA sequencing. Molecular cloning provides scientists with an essentially unlimited ... Many useful proteins are currently available as recombinant products. These include--(1) medically useful proteins whose ... 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 ...
*  Jürgen Brosius
Protein sequence analysis: automated microsequencing. Science. 1983 Feb 11;219(4585):650-9. Brosius J, Dull TJ, Sleeter DD, ... Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 1993 Nov ... This method was shortly thereafter superseded by automated protein sequencing operating in the low picoMol range. From 1977- ... There, he sequenced the first large ribosomal RNAs via their genes utilizing the Maxam-Gilbert sequencing method. It took ~2.5 ...
*  C3orf14
Combet C, Blanchet C, Geourjon C, Deléage G (March 2000). "NPS@: network protein sequence analysis". Trends in Biochemical ... This protein is also predicted as a DNA binding protein. The protein may assume a tertiary structure of a coiled coil. ... protein name). The mRNA is composed of 6 exons, and encodes a 15007.84 kD protein known as HT021. This protein has a pre- ... Pruitt KD, Tatusova T & Maglott DR (January 2007). "NCBI reference sequences (RefSeq): a curated non-redundant sequence ...
*  David Tudor Jones
Jones, David Tudor (1993). Structural approaches to protein sequence analysis. london.ac.uk (PhD thesis). University of London ... Jones's main research interests are in protein structure prediction and analysis protein folding, transmembrane protein ... The input is an amino acid sequence with unknown protein structure, then THREADER will output a most probable protein structure ... a method of protein modeling, which is used to model those proteins which have the same fold as proteins of known structures. ...
*  List of mass spectrometry software
Tannu, Nilesh S; Hemby, Scott E (2007). "De novo protein sequence analysis of Macaca mulatta". BMC Genomics. 8: 270. doi: ... Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry. In protein ... "An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database". J Am Soc Mass ... "Probability-based protein identification by searching sequence databases using mass spectrometry data". Electrophoresis. 20 (18 ...
*  Michael Levitt
Brenner, S. E.; Koehl, P.; Levitt, M. (2000). "The ASTRAL compendium for protein structure and sequence analysis". Nucleic ... Gerstein, M.; Levitt, M. (1997). "A structural census of the current population of protein sequences". PNAS. 94 (22): 11911- ... Michael Levitt publications indexed by Google Scholar Levitt, Michael (1972). Conformation analysis of proteins (PhD thesis). ... Levitt, M. (1976). "A simplified representation of protein conformations for rapid simulation of protein folding". Journal of ...
*  Proline-rich protein 30
"PredictProtein - Protein Sequence Analysis, Prediction of Structural and Functional Features". www.predictprotein.org. ... "Methods and algorithms for statistical analysis of protein sequences" Proc. Natl. Acad. Sci. U.S.A. 89, 2002-2006. Volker ... Proline-rich protein 30 (PRR30 or C2orf53) is a protein in humans that is encoded for by the PRR30 gene. PRR30 is a member in ... The Phyre2 web portal for protein modeling, prediction and analysis Kelley LA et al. Nature Protocols 10, 845-858 (2015) Dunker ...
*  Tandem mass spectrometry
Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (June 2004). "Peptide and protein sequence analysis by electron transfer ... Tandem mass spectrometry can be used for protein sequencing. When intact proteins are introduced to a mass analyzer, this is ... "Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases". Proceedings ... Tandem mass spectrometry can produce a peptide sequence tag that can be used to identify a peptide in a protein database. A ...
*  Kimmen Sjölander
She is well known for her work on protein sequence analysis. Sjölander did both her undergraduate and graduate work at the ... Sjölander is most well known for her work in phylogenomic methods for protein sequence analysis, including machine learning ... a method for improved detection of weak but significant protein sequence homology", Bioinformatics, 12 (4): 327-345 . "Kimmen ... 2001), "The sequence of the human genome", Science, 291 (5507): 1304-1351 . Krogh, Anders; Brown, Michael; Mian, Saira; ...
*  Joshua Coon
"Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry". Proc. Natl. Acad. Sci. U.S.A. 101 ( ...
*  Lysyl endopeptidase
"Use of endoproteinase Lys-C from Lysobacter enzymogenes in protein sequence analysis". Anal. Biochem. 134: 347-354. doi:10.1016 ... Ohara, T.; Makino, K.; Shinagawa, H.; Nakata, A.; Norioka, S.; Sakiyama, F. (1989). "Cloning, nucleotide sequence, and ...
*  Grapevine fanleaf virus
Sequence analysis and coat protein cistron location". The Journal of General Virology. 71 ( Pt 7) (7): 1433-1441. doi:10.1099/ ... is cleaved into three proteins. The coat protein derives from RNA2 and forms the icosahedral capsid of 60 identical protein ... The virus has an RNA genome contained on two RNA molecules, each of which is covalently attached to a small protein (the viral ... The longer polyprotein (the product of RNA1) is cleaved into five functional proteins, including the viral RNA polymerase and ...
*  Endoproteinase Lys-C
"Use of endoproteinase Lys-C from Lysobacter enzymogenes in protein sequence analysis". Analytical Biochemistry. 134 (2): 347-54 ... This enzyme is naturally found in the bacterium Lysobacter enzymogenes and is commonly used in protein sequencing. Lys-C ... Endoproteinase Lys-C is a protease that cleaves proteins on the C-terminal side of lysine residues. ...
*  ARHGDIB
"Sequence analysis of proteins separated by polyacrylamide gel electrophoresis: towards an integrated protein database". ... Identification of a non-cytosolic GDI protein interacting with the small GTP-binding proteins RhoB and RhoG". J. Biol. Chem. ... Li X, Bu X, Lu B, Avraham H, Flavell RA, Lim B (2002). "The hematopoiesis-specific GTP-binding protein RhoH is GTPase deficient ... Rho GDP-dissociation inhibitor 2 is a protein that in humans is encoded by the ARHGDIB gene. Aliases of this gene include ...
*  Bioinformatic Harvester
... provide online sequence analysis for a single protein. Harvesters search index is based on the IPI and UniProt protein ... "protein kinase binding" Protein: "Q9NPD3" Protein domain: "SH2 sar" Protein Localisation: "endoplasmic reticulum" Chromosome: " ... predicts protein localisation HomoloGene, compares proteins from different species gfp-cdna, protein localisation with ... "cDNA sequencing project" Biological databases Entrez European Bioinformatics Institute Human Protein Reference Database ...
*  Systolic array
They are also used for dynamic programming algorithms, used in DNA and protein sequence analysis. A systolic array typically ... DPUs perform a sequence of operations on data that flows between them. Because the traditional systolic array synthesis methods ... The data streams entering and leaving the ports of the array are generated by auto-sequencing memory units, ASMs. Each ASM ... addressed and sequenced under the control of the CPU's program counter (PC), the individual nodes within a systolic array are ...
*  PROSITE
... offers tools for protein sequence analysis and motif detection (see sequence motif, PROSITE patterns). It is part of ... PROSITE's uses include identifying possible functions of newly discovered proteins and analysis of known proteins for ... PROSITE is a protein database. It consists of entries describing the protein families, domains and functional sites as well as ... Uniprot - the universal protein database, a central resource on protein information - PROSITE adds data to it. InterPro - a ...
*  Baum-Welch algorithm
Durbin, Richard (23 April 1998). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge ... This is equivalent to the number of times state i is observed in the sequence from t = 1 to t = T − 1. b i ∗ ( v k ) = ∑ t = 1 ... Feature analysis is first undertaken on temporal and/or spectral features of the speech signal. This produces an observation ... Finally, semantic analysis is applied and the system outputs the recognized utterance. A limitation of many HMM applications to ...
*  40S ribosomal protein S27
"The human ribosomal protein genes: sequencing and comparative analysis of 73 genes". Genome Research. 12 (3): 379-90. doi: ... "Primary structures and sequence analysis of human ribosomal proteins L39 and S27". Biochemistry and Molecular Biology ... 40S ribosomal protein S27 also known as metallopan-stimulin 1 or MPS-1 is a protein that in humans is encoded by the RPS27 gene ... The protein belongs to the S27E family of ribosomal proteins. It contains a C4-type zinc finger domain that can bind to zinc. ...
*  Probabilistic context-free grammar
1998). Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press. ISBN 978-0 ... Dyrka, W; Nebel, J-C (2009). "A Stochastic Context Free Grammar based Framework for Analysis of Protein Sequences". BMC ... usage in the field of protein sequence analysis has been limited. Indeed, the size of the amino acid alphabet and the variety ... As a consequence, most applications of formal language theory to protein analysis have been mainly restricted to the production ...
*  Prion pseudoknot
"Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching". Nucleic Acids Res. 29 (3 ... It has been suggested that this element has a possible effect in prion protein translation. The human prion protein contains 5 ... The prion pseudoknot is predicted RNA pseudoknot structure found in prion protein mRNA. ...
*  60S ribosomal protein L39
1997). "Primary structures and sequence analysis of human ribosomal proteins L39 and S27". Biochem. Mol. Biol. Int. 40 (3): 611 ... 2002). "The Human Ribosomal Protein Genes: Sequencing and Comparative Analysis of 73 Genes". Genome Res. 12 (3): 379-90. doi: ... The protein belongs to the S39E family of ribosomal proteins. It is located in the cytoplasm. In rat, the protein is the ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...
*  Protein engineering
Without structural information about a protein, sequence analysis is often useful in elucidating information about the protein ... These techniques involve alignment of target protein sequences with other related protein sequences. This alignment can show ... and BALIBASE in order to cross reference target protein sequences with known sequences. Multiple sequence alignment techniques ... This knowledge of existing protein structure assists with the prediction of new protein structures. Methods for protein ...
*  UCKL1
2002). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 (6866): 865-71. doi:10.1038/414865a. ... 2006). "A probability-based approach for high-throughput protein phosphorylation analysis and site localization". Nat. ... 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/ ...
*  Stephen Altschul
Altschul is the co-author of the BLAST algorithm used for sequence analysis of proteins and nucleotides. Altschul graduated ... His research interest is centered on sequence alignment algorithms, statistics of sequence comparison and measurement of ... Aspects of Biological Sequence Comparison (PhD thesis). Massachusetts Institute of Technology. Death notice of Arthur Goodhart ... A new generation of protein database search programs". Nucleic Acids Research. 25 (17): 3389-3402. doi:10.1093/nar/25.17.3389. ...