... Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> . ... 1 allpy ( 1 . ... 5 -- Danya Alexeyevsky < dendik @ kodomo . fbb . msu . ... 15 * blocks3d - wt : create / var / run / wt by initscript , as required by new Debian policy . ... 40 * Fixed debian / changelog . ... 46 * New allpy release . ... 93 * Debianized blocks3d , blocks3d - wt ; fixed debian dependencies for . ... 102 -- Danya Alexeyevsky < dendik @ kodomo . ... 104 allpy ( 0 . ... 108 -- Danya Alexeyevsky < dendik @ kodomo . ...

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• allpy: d87129162eb4 debian/changelog
• allpy: fdc2d3594a3e debian/changelog
• allpy: 9c00d065c054 debian/changelog

... 2011/12/09 . ... added alignment merging . added parameter corresponding to the width of output alignment . fixed homologue searching for very long query sequences . ... Copyright 2010-2011 Yury Pekov ...

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gBioSeq . gBioSeq is a graphical multiple DNA sequence alignment editor for GTK/Linux. It provides an easy to use interface to manual alignment, seach as SeqApp on Macintosh. Sorry, it is only available in french for the moment. ... http://www.cnrs-gif.fr/pge/bioinfo/gbioseq . ... Available Binary Packages: . ... Mailing list information at http://www.cnrs-gif.fr/pge/bioinfo/listef.html . ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ...

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• SAL- Other Scientific Fields - Chemistry, Biology Related - GDE
• SAL- Other Scientific Fields - Chemistry, Biology Related - SC_rate
• SAL- Other Scientific Fields - Chemistry, Biology Related - DCSE

... 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
• PLANdbAffy: probe-level annotation database for Affymetrix expression
• NPG-explorer

README for XFree86 on OS/2 : Installing the packages . Previous: Checking Compatibility of Video Hardware . Next: Adding Variables to CONFIG.SYS . XFree86/OS2 assumes a directory hierarchy starting from drive:\XFree86 . ... You might encounter that some packages report duplicate files, e.g. the X server packages install corresponding README files, which are also in the Xdoc package. This is okay, the files are the same. Let unzip replace the files. ...

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• Installing the System

Maximum RPM: Taking the Red Hat Package Manager to the Limit . ... One or more RPM package files (URLs OK) . ... Install documentation . ... the section called --replacefiles : Install the Package Even If It Replaces Another Package's Files . ... RPM turns that process into a single command. rpm -i ( --install is equivalent) installs software that's been packaged into an RPM package file. ... Every time RPM installs a package on your system, it keeps track of the files it installed, in its database. ...

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• LanguageSetup - UNИX
• A Few Handy Queries
• Performing an Install

... О UNИX . ... LanguageSetup . ... MoinMoin comes with no system and help pages installed by default (the page you read right now is the only page after a fresh installation). ... You can install help and system page packages for any language you want to support for your wiki users. ... For the root URL of your wiki, moin will use a special page (called the "front page"). ... If English is not your wiki's main language, choose something in YOUR wiki language page_front_page = u"MyStartingPage" . ...

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• HelpOnPackageInstaller - UNИX
• HelpOnInstalling/TwistedWeb - UNИX

... OK ======================================= To compile CompHEP input make command ======================================= make # command output : ****************************************************************** * CompHEP -4.4p3 has been successfully built * * * * Please create a user working directory using the command * * make setup WDIR=path_to_your_user_work_dir * * NOTE: Do not use '~' to refer to home ... CompHEP-interfaces-1.0.1 has been installed successfully!! ...

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... This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows. The Overview page is the front page of this API document and provides a list of all packages with a summary for each. ... Each package has a page that contains a list of its classes and interfaces, with a summary for each. ... Each of these pages has three sections consisting of a class/interface description, summary tables, and detailed member descriptions: . ...

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• API Help
• : Class Hierarchy
• : Package ucar.multiarray

... The boards can be used to create very large clusters with outstanding communication performance. SSP Contents ------------ A short description of the files and catalogues in the SSP : README - this file HW - how to install the SCI boards OS - how to configure the operating system before installing the SSP doc - some extra documentation pkg - all the software distribution files bin - binaries used during installation install - the SSP installation program uninstall - the ...

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... All contacts alignment . ... Blue background means a contact with backbone phosphate. ... HBond with major groove + contact through a molecule of water with backbone phosphate; . ... contacts through water molecules both with backbone phosphate and major groove; . ... HBond with major groove + contacts through water molecules both with backbone phosphate and major groove; . ... HBond with major groove + engagement in hydrophobic cluster + contact through a molecule of water with backbone phosphate; ...

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• SVETKA, a program for multiple sequence alignments analysus
• SVETKA, a program for multiple sequence alignments analysis
• SDP home page

Using stand-alone SDPfox . ... To add a new specificity group, type in the group name and press "Add" . To change composition of specificity groups, select two groups: first, from which to remove sequences, and second, to which to add sequences. ... For a constructed grouping, it is possible to run SDPgroup, re-randomize grouping or move sequences according to the best weights (see algorithm) under the link 'SDPgroup'. ... These sequences are likely to be re-grouped after SDPgroup is performed. ...

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• RNA Alignment
• Input Formats
• SDPpred

install ]] . ... Installation of a user directory . ... Below, we use the following notations: XXXX - CompHEP version number; comphep-XXXX - directory where CompHEP files will live; comphep-XXXX.tgz - distributive tar-file with sources; comphep-XXXX-linux.tgz - distributive tar-file with binaries; . ... The directory with name comphep-XXXX will be created with all files of CompHEP distributive. ... In order to create a user working directory execute: make setup WDIR=path_to_user_work_directory . ...

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• news [CompHEP]
• overview [CompHEP]
• download:main [CompHEP]

Scoring Matrices . Matrix Sequences Sequence Consisting of the first four Amino Acids in the Protein GYRB_ECOL: . ... Sequence Achieved by Substitution of the 2nd and 4th Amino Acid and Insertion between the 3d and 4th Amino Acid, in the Protein GYRB_ECOLI, to randomly chosen new amino acids: . ... Matrix Sequences Sequence Consisting of the First Nine Amino Acids of the Protein GYRB_ECOLI: . ... Sequence Consisting of 2nd, 3d, 7th, 8th and 9th Amino Acid Residues of the Protein GYRB_ECOLI: . ...

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• Множественное выравнивание.
• alignment

Электронная библиотека Попечительского совета . ... Korf I., Yandell M., Bedell J. - Blast (Basic Local Alignment Search Tool) . ... Название: Blast (Basic Local Alignment Search Tool) . Авторы: Korf I., Yandell M., Bedell J. Аннотация: . ... BLAST (Basic Local Alignment Search Tool), is a sophisticated software package for rapid searching of nucleotide and protein databases. ... BLAST is the only book completely devoted to this popular suite of tools. ... BLAST basics and the NCBI web interface . ...

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• Brown S.M. - Bioinformatics: A Biologist's Guide to Biocomputing and the
• Althaus E. - A branch-and-cut algorithm for multiple sequence alignment ::
• Lathrop R.H., Rogers Jr R.G., Smith T.F. - A Bayes-optimal sequence-structure

... This section contains notes and hints specific to installing PHP on OpenBSD . ... Then simply find out which flavors you wish to install, and issue the make install command. ... OpenBSD Ports Install Example . cd /usr/ports/www/php4 $ make show VARNAME=FLAVORS (choose which flavors you want from the list) $ env FLAVOR="imap gettext ldap mysql gd" make install $ /usr/local/sbin/php4-enable . There are pre-compiled packages available for your release of OpenBSD . ... Unix/Mac OS X installs . ...

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• Unix/Linux installs
• Unix/Mac OS X installs
• Unix/Solaris installs

There are the following elements of the user interface in the CompHEP package: On-line Help, Menu, Message, String Editor, Table Editor, Diagram Viewer and Plot Viewer . You can control them using the Arrows keys, Enter , Esc 1 , Backspace , PgUp / PgDn 2 keys and the mouse click. CompHEP is sensitive to the left mouse button release. ... 1 Use the 'Ctrl [' sequence if the Esc key is absent on your keyboard . ... On-line Help. Menu. ... String Editor. ... Diagram Viewer. Plot Viewer. ...

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• CompHEP/SUSY
• Install
• [Comphep-common] Events to produce of LHAEF format

... MY_HASH } MY_P = T-COFFEE_distribution_Version_${ MY_PV } DESCRIPTION= A multiple sequence alignment package HOMEPAGE= http ://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html SRC_URI= http ://www.tcoffee.org/Packages/Stable/Version_${ MY_PV }/${ MY_P }.tar.gz LICENSE = GPL-2 SLOT= 0 KEYWORDS= ~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux IUSE= ...

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• http://mirror.msu.net/pub/gentoo-portage/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild
• http://mirror.msu.net/pub/gentoo-portage/sci-biology/pysam/pysam-0.9.0.ebuild
• http://mirror.msu.net/pub/gentoo-portage/eclass/elisp.eclass

... Bioinformatics Portal . GeneBee . ... Bioinformatics Portal of A.N.Belozersky Institute, . Moscow State University . Supported by the Russian Foundation for Basic Research, grant 13-07-00969-a . Original Services of GeneBee Group . Databanks screening . Sequence analysis . Screening by keywords . AliBee Multiple alignment Release 3.0 . AliGraf Graphical Alignment . AliComp Alignments Comparison . Screening by similarity Release 3.0 . ...

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• RNA secondary structure prediction
• BLAST Basic Overview
• GeneBee service

NGS Data Analysis with Unipro UGENE Olga Golosova, Yuriy Vaskin, German Grekhov, Yuliya Algaer UNIPRO, Lavrentieva ave. ... That is where Unipro UGENE NGS framework comes in play. ... Moreover, the UGENE toolkit allows one to automate common tasks by creating workflows with the integrated tools using the UGENE Workflow Designer. Analysis of NGS data with UGENE may start, for example, from quality control of raw NGS data, received from a sequencing facility, with the integrated FastQC [3] tool. ...

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• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/215.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/18.pdf