Электронная библиотека Попечительского совета . ... Althaus E. - A branch-and-cut algorithm for multiple sequence alignment . ... Название: A branch-and-cut algorithm for multiple sequence alignment . Автор: Althaus E. Язык: . ... Электронная библиотека попечительского совета мехмата МГУ , 2004-2016 . ...

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... Alternative core new atoms (%) . ... An alignment of a set of structures is a set of positions , to each position some atoms from different structures correspond. ... Geometrical core of a set of structures is a subset of alignment positions those atoms are disposed similarly in all structures. ... For any two positions included into geometrical core, the distances between CA atoms of those positions in all structures may differ not more than the value of the parameter "Distance spreading". ...

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... Algorithm & . Format requirements . ... SDPsite is a tool for identification of protein active and other functional sites, based on spatial clustering of SDPs (specificity-determining positions, described here ) with CPs (conserved positions). ... Mapping predictied positions onto structure and construction of the best cluster . ... The input data of the algorithm are a multiple protein alignment divided into specificity groups . ... is called statistical significance of the set of k* positions . ...

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• RNA Alignment
• SDPsite
• Site Cluster

... 4 from monomer import AminoAcidType . ... 18 """ Sequence of Monomers . ... 21 * name -- str with the name of sequence . ... 24 * pdb_chains -- list of Bio.PDB.Chain's . ... 27 * pdb_residues -- dictionary like {Bio.PDB.Chain: {Monomer: Bio.PDB.Residue}} . ... 42 def __init__ ( self , monomers = None , name = '' , description = "" ): . ... 106 return Sequence ( monomers , name , description ) . ... 189 def pdb_has ( self , chain , monomer ): . ... 192 def secstr_has ( self , chain , monomer ): . ...

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• allpy: 675b402094be lib/block.py
• allpy: fb3164f03984 lib/sequence.py
• allpy: 675b402094be lib/sequence.py

... If there's no significant multiple alignment , including the sequence, that you interest, then the secondary structure is built, using only the energy model (just the potential energy of the system is minimized), but very often such method will give unreliable results. ... It should be mentioned that by default, at alignment case, the RNA secondary structure will be predicted for the first sequence of the alignment. ... It is done through optimizing, not the real, but model energy of the structure. ...

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• OUTPUT
• Screening of pattern or alignment against PROTEIN databank
• Screening protein sequence against PROSITE databank

... Criteria of branch quality . As it was repeatedly told , phylogenetic trees consist from branches. ... I. e., those positions, which can separate sequences of the branch from other sequences in the alignment. ... Measure of branch separation . ... Here and further: A - branch of the tree, i , j - sequences of alignment . ... That's why number of conserved positions in some branch should be considered in complex with the distribution of conserved positions in the whole alignment. ...

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• About this project
• Inquiry information || Distances
• Inquiry information || Parsimony algorithm

... Minimal size of Clud clusters (residues) . ... An alignment of a set of structures is a set of positions , to each position some atoms from different structures correspond. ... Hydrophobic cluster of a single protein structure is a separated pool of nonpolar atoms. Usually there is the biggest cluster in the protein called hydrophobic core. ... ConClus program is able to detect of conservative hydrophobic clusters for a family of related protein domains or just for a set of aligned proteins. ...

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• Nhunt: program for nucleic acid sequence similarity search
• StructAlign help

Application of evolutionary model in the evaluation of the quality of pair wise alignment of amino acid sequences Valery Polyanovsky, V. G. Tumanyan Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia ... : polyanovskyvo@mailfrom.ru, tuman@eimb.ru The purpose of the work is to develop a universal method for estimating the pairwise alignment quality depending on the evolutionary distance (degree of homology) between the ... REFERENCES 1. ...

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• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/161.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/215.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/179.pdf

... Block DNA GyrB" shows the score of pairs Lys|Lys, Lys|Arg and Lys|Ser respectively, from a block constituted by amino acid sequences from the same protein (DNAGyraseB), but from different organisms, for example GYRB_ECOLI, GYRB_YERPE (yeast), GYRB_HEINE, GYRB_MUSC (mouse). Block 200 illustrates the score of these pairs from 200 different blocks constituted by sequences from differnet organisms. ... Between the values of single BLock the differences are smaller than between the values of Blosum62. ...

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• Conservative Amino Acid Residues
• Structure Alignment

Routing on lattice-cellular structures" . Ryabov G.G. An extension of the class of lattice graphs is considered. In order to become close to the Euclidean metric, inclusion of additional ribs with weights equal to the corresponding lengths of vectors in the Euclidean space is performed in a neighborhood on the lattice. ... An algorithm for constructing a set of the shortest paths on such a lattice is proposed. ... PostScript (in Russian) (6.04MB) . PDF (in Russian) (710KB) . ...

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• A variable structure algorithm using the (3,2)-scheme and the Fehlberg method
• "Enclosure structures of equal level line fields in the gradient filling

DCSE . DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor. ... It offers lots of features such as color display of characters and structure, automatic alignment relative to sequences already aligned with others, sequence grouping, sequence or pattern searching, marker system and checking of incorporated RNA structure. tkDCSE is a version of DCSE for X-Windows. ... Home Site: . ... None . ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ...

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• SAL- Other Scientific Fields - Chemistry, Biology Related - GeneMine
• SAL- Other Scientific Fields - Chemistry, Biology Related - HMMER
• SAL- Other Scientific Fields - Chemistry, Biology Related - PHYLIP

Institute Adress: . ... Moscow, 119071, RUSSIA . fax (7-495) 954-55-34; admin@sevin.ru . ... tel. (7-495) 952-20-88, (7-495) 952-73-05; . ... Alexey V. Surov, Dr. Biol. Sci. , . ... tel. ... The Institute of ecology and evolution of the Russian Academy of Sciences established in 1934 by academician A.N. Severtsov is one of the leading biological institutes of Russia. ... The Institute coordinates programs of Russian Academy of Sciences: “Biodiversity” and “Biological resource of Russia”. ...

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• Parasitology: Laboratory for Experimental Parasitology: Goals and Tasks

This home page belongs to small group of scientists working at . Sternberg Astronomical Institute which is a part of Moscow State University . ... Электронная библиотека научно-технической и художественной литературы (доступна только из ГАИШ) . ... Local staff . Dr. Edward Kononovich (konon -at- sai.msu.ru), Associate Professor . ... Dr. Sergey Ayukov (asv -at- sai.msu.ru), Research Fellow, Webmaster of the group . ... Joint seminar of Solar Studies Structure Group and Solar Photometry Group . ...

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... The LanHEP input file is the sequence of statements, each starts with a special identifier (such as parameter, lterm etc) and ends with the full-stop ' . ... This section is aimed to clarify the syntax of LanHEP input files, i.e. the structure of the statements. ... Let us consider the LanHEP input files for the Standard Model with both the t'Hooft-Feynman and unitary gauges. ... LanHEP allows the user to define several keys , and use these keys to branch among several variants of the model. ...

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• General structure

... Derived datatypes . Up: Point-to-Point Communication Next: Datatype constructors Previous: Null processes . ... Instead, MPI provides mechanisms to specify more general, mixed, and noncontiguous communication buffers. ... More general communication buffers are specified by replacing the basic datatypes that have been used so far with derived datatypes that are constructed from basic datatypes using the constructors described in this section. ... A sequence of basic datatypes . ... Центры . ...

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Key-words: rhythm, stress, syllable, rhythmic structure, syntagm, utterance, prosody, speech production, speech perception . ... In speech communication, RS are both units of speech production and speech perception. ... The research of speech rhythm in diachrony and synchrony consists of the analysis and the description of speech rhythmic units concerning Old Church Slavonic, Old Russian, Old High German in diachrony and Modern Russian, German, Czech and Bulgarian in synchrony. ...

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... Геология >> Геотектоника | ... Добавить новое сообщение . ... Учебное пособие "Введение в тектонофизику". Гончаров М. А., Талицкий В. Г., Фролова Н. С. Ответ. ... Тезисы научной конференции ЛОМОНОСОВСКИЕ ЧТЕНИЯ, ноябрь 2011 года СЕКЦИЯ ГЕОЛОГИЯ: . ...

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... MATHEMATICAL AND SYSTEM BIOLOGY UDC 577.1 Membrane Profile-Based Probabilistic Method for Predicting Transmembrane Segments via Multiple Protein Sequence Alignment R. A. Sutormina and A. A. Mironova a b , b, c State Research Center GosNIIgenetika, Moscow, 117545 Russia; e-mail: sutor_ra@mail ... Bioinformatics, Moscow State University, Moscow, 119992 Russia Received January 25, 2006 Abstract--Prediction of transmembrane (TM) segments of amino ... Protein Sci. ... Proteins. ...

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• http://storage.bioinf.fbb.msu.ru/~roman/Sutormin_CV_aug2014.pdf
• http://storage.bioinf.fbb.msu.ru/~roman/Sutormin_CV_aug2013.pdf

... The real structure (dislocation density, inclusions, segregations, character of distribution of components) was studied in PbTe crystals doped with Cr, Co, Ni, and In. The relation between the real structure of crystals and the features of the T-x phase diagrams of the corresponding systems, doping level, and the rates of growth and cooling was established. ... Tiller criterion was used to calculate the concentration range of stability of a crystallization surface during the crystal growth. ...

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• The Molecular Structure of 2-Chloroacrolein Studied by Gas Electron
• Structure of the Chemistry Department of Moscow State University
• Moscow University Chemistry Bulletin Vol. 53, No. 2, P. 81 (2012)

... In the present-day Russia it quickly gives rise to the following question: "Who benefits from enforcing powerful structures in Russia?" ... Now all these structures will stay in place with new district structures, several times as big, built above them. ... As a conclusion, it should be stated that the people should benefit from enforcing the powerful structures in Russia in the first turn, only then the reforms taking place in our country could be considered fully democratic. ...

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