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

Given word length and max number of mismatches . Use MEME algorithm for define conserved blocks . Apply the Dynamic programming algorithm to create chain of the blocks . Refine the chain using combined profile for chain of blocks. ... Reduce word length and number of mismatches and repeat the procedure for spacer between the blocks. ... Create helix profile and apply MEME-like iterative procedure to find sets of helices that consistent lokated reative to conserved blocks . ...

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• SDPsite - Algorithm Format requirements
• Algorithm
• SDPlight

Geometrical core (core) is a maximal set of alignment positions such that C atoms in these positions are disposed similarly in ALL input protein chains. ... Minimal core size (#aa's) . ... Alternative core new atoms (%) . ... Geometrical core is a maximal set of alignment positions such that C atoms in these positions are disposed similarly in ALL input protein chain. ... Each input sequences is aligned to the corresponding sequence obtained from the ATOM section of the protein chain in the PDB file. ...

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• SVETKA, a program for multiple sequence alignments analysis

... HELP ON SCREENING OF PATTERN OR ALIGNMENT AGAINST PROTEIN PROTEIN . ... The method of looking for all pattern entries (possibly inexact) in PROTEIN databank is almost the same as in PROSITE screening procedure. ... The screening by query alignment, based on the same principle: the alignment is seen as a pattern defining letter's frequencies in every position. The pattern example: . ... the only one capital letter at a position means that only given residue should be at the position. ...

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• OUTPUT
• IGLA-3D User Guide
• RNA secondary structure prediction

. SDPpred: a tool for prediction of amino acid residues . that determine differences in functional specificity of homologous proteins .

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

SDPpred: Results . ... The number of proteins in the alignment: 21 . The alignment length: 988 . 38 SDPs predicted . Cutoff probability: 1.85e-171 . ... Amino acid residues in SDPs for protein PMS1_HUMAN PMS2_HUMAN PMS2_MOUSE PMS1_SCHPO PMS1_YEAST MUTL_THEMA MUTL_AQUAE MUTL_AQUPY MUTL_BORBU HEXB_STRR6 MUTL_BACSU MUTL_RICPR MLH1_HUMAN MLH1_YEAST MUTL_CHLPN MUTL_CHLTR MUTL_ECOLI MUTL_HAEIN MUTL_SYNY3 MUTL_TREPA MUTL_THEAQ . ... Protein Sci 13(2): 443-56. ...

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• GeneBee service result
• Матрицы переходов
• Global and Local Alignment of A.A Sequences

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/2013/abstracts/abstracts/245.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/120.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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• SAL- Other Scientific Fields - Chemistry, Biology Related - GeneMine

... 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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• Align tool for DNA-protein complexes

... Thu, 16 Dec 2010 19:24:22 +0300 . Daniil Alexeyevsky . ... Removed controversial methods of allpy.base.Alignment: length, height, identity . ... Moved allpy.base.Alignment.muscle_align to allpy.protein . ... Wed, 15 Dec 2010 23:45:11 +0300 . ... Tue, 14 Dec 2010 21:06:42 +0300 . ... Moved contents of block.py to base.py without any changes. ... Moved contents of allpy._monomer to allpy.base . Sat, 04 Dec 2010 00:19:17 +0300 . ... Fri, 03 Dec 2010 23:24:43 +0300 . ... allpy: add base.py 1.1.0 . ...

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• allpy: log
• allpy: 27e866560087 test/usecase1.py
• allpy: 53690e470eff test/usecase2.py

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/gentoo-portage/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild
• http://mirror.msu.net/pub/gentoo-portage/sci-chemistry/mustang/mustang-3.2.2.ebuild

1== 1_EC_PurR -------- matikdvakranvstttvshvinktr --- fvaeetrnavwaaikelhyspsavarslkvnhtksigllatsse ------aayfaeiieavekncfqkgytlilgnawnnlekqraylsmmaqkrvdgllvmcseypepllamleeyrhipmvvmdwgeakad-ftdavidnafeggymagrylierg--hreigvipgplerntg ... -hrptavfcggdimamgalcaademg---lrvpqdvsligydnvrnaryftpalttihqpkdslgetafnmlldrivnkre--------epqsievhprlierrsvadgpfrdyrr--- 1_STY1692 -------- matikdvakranvstttvshvinktr --- ...

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

Alignment in free decaying MHD turbulence" . ... Using a shell model of turbulence, we have investigated a long-time evolution of magnetic and velocity fields in the MHD turbulence with various types of initial states. ... For most realizations, a coherent state with high alignment between the magnetic and velocity fields has been developed. In the case of establishment of the coherent state, the dissipation rate of energy is found to be substantially reduced. ...

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• Contents.Volume 1
• "Adjustment of lithofacial models with a modified simulated annealing...
• "Heuristic algorithms of mapping MPI-programs onto multicluster computer and

... О UNИX . ... HelpOnImages . Неизменяемая страница . ... Working With Images . ... If you just want to get an image on a page, simply upload the image file (using the 'Attachments' link). ... For example, if you put large image {{attachment:duckie.png}} into the middle of a paragraph, like this , then that's exactly what you'll get. ... This example uses a chair image that's aligned left. Notice that paragraph text flows around it, so you can (for example) stagger images on the page. ...

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• HelpOnTables - UNИX
• WikiCourse/15 Tables - UNИX

The QGroupBox widget provides a group box frame with a title. ... QGroupBox  ( QWidget * parent=0, const char * name=0 )  . QGroupBox  ( const char * title, QWidget * parent=0, const char * name=0 )  . const char*  title  () const . ... int  alignment  () const . ... Constructs a group box widget with no title. ... Constructs a group box with a title. ... Returns the alignment of the group box title. ... Sets the alignment of the group box title. ... Sets the group box title text to title. ...

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• Qt Toolkit - QBoxLayout Class
• Qt Toolkit - QLabel Class

... О UNИX . ... HelpOnImages . Неизменяемая страница . ... Working With Images . ... If you just want to get an image on a page, simply upload the image file (using the 'Attachments' link). ... For example, if you put large image {{attachment:duckie.png}} into the middle of a paragraph, like this , then that's exactly what you'll get. ... This example uses a chair image that's aligned left. Notice that paragraph text flows around it, so you can (for example) stagger images on the page. ...

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• HelpOnTables - UNИX
• WikiCourse/15 Tables - UNИX

Welcome , Registration , and other StartingPoints ; TWiki history & Wiki style; All the docs.. ... TablePlugin 10 - 2002-03-07 - PeterThoeny . ... Table cell spacing. ... Set CELLSPACING = 1 . ... 05 Jan 2002 PTh: Fixed sorting bug of cells with leading white space . 06 Dec 2001 PTh: Fixed date sorting bug . 03 Dec 2001 PTh: Fixed sort="off" bug and more . 29 Nov 2001: PTh fixed Perl warnings . 16 Nov 2001: PTh added table border, cell spacing, cell padding, gif files . ...

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• VarTABLE - TWiki - TWiki
• %TOPICTITLE% ( vs. 1) - TWiki
• VarTABLE - TWiki - TWiki - (printable)

This diagram shows how the 'vertical-align' properties on cells combine to determine the height of the row containing the cells. The diagram also illustrates the meaning of some values of 'vertical-align' that apply to table cells: baseline, top, bottom, and middle. The diagram shows a row of five (labeled) table cells of varying heights and alignments. ... The first cell is aligned with the row baseline and extends to just below the row top. ...

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• Alignment, font styles, and horizontal rules in HTML documents
• Y. Meyer, 1993, Wavelets: Algorithms and Applications, S.I.A.M.
• Index

... Planets In The Sun . ... Credit Copyright: SOHO - LASCO Consortium, ESA , NASA Explanation: Today , all five naked-eye planets (Mercury, Venus, Mars, Jupiter, Saturn) plus the Moon and the Sun will at least approximately line-up. ... And what about the Moon ? ... Publications with keywords: Jupiter - Mars - planet - Saturn - Sun - planetary alignment - Moon . Publications with words: Jupiter - Mars - planet - Saturn - Sun - planetary alignment - Moon . ... Neon Saturn . ... Moons and Jupiter . ...

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• Journal "Peremennye Zvezdy"
• Planets Above The Clouds
• Venus, Moon, and Neighbors

... Two algorithms: the principal component's method (MPC) and median polishing (Median) are applied for that [2-3] . The algorithm of median polishing was offered by John W. Tukey (1981), and was applied after modification by E.V.Pervago for processing of Resistivity Imaging or Total Electrical Sounding (TES) data. ... To this table we apply algorithm of median polishing, but in addition to rows and columns we shall also include in processing inclined lines, corresponding to C-effect. ...

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