... 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

... 6 import sequence . ... 19 * self.alignment -- alignment object, which the block belongs to . ... 22 * self.positions -- list of positions of the alignment.body that . ... 25 Don't change self.sequences -- it may be a link to other block.sequences . ... 34 def __init__ ( self , alignment , sequences = None , positions = None ): . ... 75 If more than one pdb chain for some sequence provided, consider all of them . ... 129 alignment_sequence = self . ... 136 def sequences_chains ( self ): . ...

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• allpy: 2deb7942fbed lib/block.py
• allpy: 35537fc8d5be allpy/block.py
• allpy: 5a089847d42e lib/project.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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• IGLA-3D User Guide
• BLAST Frequently Asked Questions (FAQ)
• BLAST Basic Overview

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/104.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/197.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/164.pdf

Evalign . Evalign is a computerised evaluation method for protein sequence alignment algorithm. It compares computer alignments with structural alignments of protein sequences and tells how correct your sequence alignment program is. It gives additional information on the characteristics of different alignment algorithms and shows types specific failings in alignment. ... None . ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ... SAL@KachinaTech.COM . ...

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SVETKA, a program for analysis of different alignments . Back to the help page . ... Such a feature can look like " Leucine in the position 362 of the alignment of the entire family " and can, in many cases, be a "decision rule" to distinguish sequences from two sides of a tree branch. ... Comparing the alignment with an input tree (the tree may be entered by the user or reconstructed with the WPGMA algorithm), the program detects supporting positions of the alignment for every branch the tree. ...

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• SDPpred
• Inquiry information || Parsimony algorithm
• SDP home page

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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• Pedersen C.N.S. - Algorithms in Computational Biology :: Электронная библиотека
• Shen A. - Algorithms and Programming :: Электронная библиотека попечительского
• Brown S.M. - Bioinformatics: A Biologist's Guide to Biocomputing and the

... 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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• SVETKA, a program for multiple sequence alignments analysis
• S : rm_systems

... 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
• Nhunt

... Values: 0 (Uncorrected); 1 (Jukes-Cantor); 2 (Kimura); 3 (Tamura); 4 (Tajima-Nei); 5 (Jin-Nei Gamma)) * -protmethod menu [0] Multiple substitution correction methods for proteins. ... Any integer value) * -calculatea boolean [N] This will force the calculation of parameter 'a' in the Jin-Nei Gamma distance calculation, otherwise the default is 1.0 (see -parametera option). * -parametera float [1.0] User defined parameter 'a' to be use in the Jin-Nei Gamma distance calculation. ...

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• Global and Local Alignment of A.A Sequences
• Матрицы переходов

Roman Sutormin rsutormin@gmail.com Professional experience 05/2013 ­ present: Lawrence Berkeley National Laboratory (Berkeley, CA, USA) Software developer Development of JSON based storage system used for keeping biological data involved in public KBase services. ... 10/2009 ­ 08/2011: Mail.Ru Group (Moscow, Russia), Software developer Support and development of data warehouse (PostgreSQL) and administration web tool (JBoss + GWT) on serverside of MMO game "Allods Online". ... 2013 Jul 1514(1):476. ...

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• http://storage.bioinf.fbb.msu.ru/~roman/mol_biol_mosk_2006.pdf
• http://storage.bioinf.fbb.msu.ru/~roman/Sutormin_CV_aug2013.pdf
• Roman Sutormin. Home Page

... The main problem is increasing the recognition rate of some recognition engines, working in some restricted domains, such as telephone time-table question-answer systems and so on. ... Our algorithms allow user to get recognition variants, which are right sentences in some formal language. ... We suppose that BRE can produce a set of recognition variants in the form of the "complex chain". ... Length of complex chain is the number of vertexes in its graph. ... const*n^2 . ...

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... About lab . ... MSU Graphics & Media Lab (Video Group) . The algorithm allows to increase video frame rate (fps) by the factor equal to any integer number. ... Frame rate conversion is done as shown on the picture below: . Frame rate conversion scheme . ... arbitrary whole number of interpolated frames between reference frames. ... Explicit scheme of occlusions detection improves visual quality of interpolated frames in areas near the frame edges. ... Video Frame Rate Double Up-Conversion . ...

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• Video Frame Rate N-Times Up-Conversion | Лаборатория компьютерной графики и
• Road monitoring | Graphics and Media Lab
• Road monitoring | Лаборатория компьютерной графики и мультимедиа

... 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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• Semantic Terms | PARALLEL.RU - Информационно-аналитический центр по

An evolutionary algorithm of feature accumulation for the construction of neural networks" . ... A description of a new algorithm for the automatic neural network construction technique that involves positive features of the evolutionary and constructive approaches is presented. The main idea of the algorithm is based on the following: at each step, a neural network is increased by adding blocks of new neurons having a maximal influence on the error reduction. ... PDF (in Russian) (1.04MB) . ...

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• "A survey of algorithms for constructing a Delaunay triangulation"
• "A parallel implementation of the subgradient algorithm for maximizing the
• "Routing on lattice-cellular structures"

. Выберите категорию обращения: Общие вопросы Отчеты Рейтинги Диссертационные советы Конкурсы Ввод данных Структура организаций Пользователи Проблемы с регистрацией\входом в систему . Тема обращения: . Описание проблемы: . Введите почтовый адрес: . Войти в систему . Регистрация . Главная . Поиск . Статистика . О проекте . Помощь . Авторы: Wahlroos T. , Atabekov J.G. , Dorokhov Y.L. , Makela M. , Korpela T. Номер: WO2004076673 . Дата публикации патента: 10 сентября 2004 г. Добавил в систему: Дорохов Юрий

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• DNA sequence : the journal of DNA sequencing and mapping - журнал | ИСТИНА -

... Another way to fend off and detect impostors is to use call sequence checks. Call sequence checks help you protect against intruders that somehow managed to find out the password you log into your UUCP system with. ... When the attacker call your UUCP feed and steals your mail, this will increase the feeds call sequence number by one. ... If you have enabled call sequence checks, you should check your log files regularly for error messages that hint at possible attacks. ...

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• MySQL Reference Manual for version 3.23.10-alpha. - H Description of MySQL

Construction of sequences of zeros and ones with complex finite sequences / A. Yu. ... Vestnik Moskovskogo Universiteta. Seriya 1. ... We construct infinite sequences of zeros and ones under some restrictions (not to contain subwords of some definite type or definite bits at definite positions, etc.) This paper concerns probabilistic methods of constructing such sequences with application of Lov sz lemma and their reformulation in terms of the Kolmogorov complexity and Martin-L f randomness. ...

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• Vestnik Moskovskogo Universiteta. Seriya 1. Matematika. Mekhanika Вестник

Distributed under the terms of the GNU General Public License v2 # $Id$ EAPI=5 inherit eutils flag-o-matic multilib toolchain-funcs EXTENSIONS = -without- extensions DESCRIPTION= Multiple sequence alignments using a variety of algorithms HOMEPAGE= http:// mafft .cbrc.jp/alignment/software/index.html SRC_URI= http:// mafft .cbrc.jp/alignment/software/${P}${ ...

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• http://mirror.msu.net/pub/gentoo-portage/sci-biology/mafft/mafft-7.215.ebuild
• http://mirror.msu.net/pub/rfc-editor/rfc-ed-all/rfc1110.txt
• http://mirror.msu.net/pub/rfc-editor/rfc-ed-all/pdfrfc/rfc1110.txt.pdf

... 2 ZERO-ORDERED SEQUENCES OF SPARSE VECTORS Let X = {xk } be a sequence of sparse vectors from Kn, I = {ik } be a sequence of multiindices. ... L ..... uL x1 ..... x1 ..... xn NNp-1 u1 u p-1 xn NNp-1 u1 NN p up-1 ..... up Let's consider a following sequential chain SPN of linked -neurons: u1 = spn1(x), up = spnp(x, up-1), 7 where p = 2, . ... We learn -neurons spn1, . ... Let's consider a following multy-layered network SPNN of -neurons: u1 = spn1(x), up = spnp(x, up-1), where p = 2, . ... SPNp-1(x))...

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