log . ... Thu, 16 Dec 2010 03:26:57 +0300 . Daniil Alexeyevsky . allpy.base.Alignment is not a list of columns, but an object with attributes: sequences, columns . ... Reimplemented allpy.base.Alignment.append_sequence . ... Wed, 15 Dec 2010 23:45:11 +0300 . ... boris (kodomo) . ... boris . ... Tue, 14 Dec 2010 21:25:22 +0300 . ... Mon, 13 Dec 2010 22:16:37 +0300 . ... Sat, 04 Dec 2010 00:19:17 +0300 . ... Fri, 03 Dec 2010 23:37:16 +0300 . ... Tue, 30 Nov 2010 17:11:25 +0300 . ...

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• allpy: allpy/base.py history
• allpy: d87129162eb4 test/usecase1.py
• allpy: d87129162eb4 test/usecase2.py

... 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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• ConClus

... Markup We sometimes (very often) want to add marks on an alignment. ... Our definitions Examples What works Projects using allpy Future Converting alignment format alignment = protein. Alignment ().append_file( input_file, format= genbank ) alignment .to_file(output_file, format= fasta ) Converting alignment format -- the uncensored version from allpy import protein input_file = open( input_file.fasta ) output_file = open( output_file.fasta , w ) alignment = protein ...

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• Global and Local Alignment of A.A Sequences
• Множественное выравнивание.

AliGraf - GeneBee Graphical Alignment Help Type in a title for this session for you to remember. ... Type in an alignment algorith name (Genebee, ClustalW, Manual.. ... Even - all column space are colored; Sparse - every column is colored with respect to the column weight: less weight more space is left uncolored; Very sparse - more space is left uncolored. ... Also you can get a picture when only selected groups are colored. ... Group set depends on selected group type. ...

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• AliComp - GeneBee Alignment Comparison Help
• AliComp - GeneBee Alignments Comparison - Advanced
• OUTPUT

... 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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• Input Formats
• SDPlight
• RNA Alignment

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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• SVETKA, a program for multiple sequence alignments analysus
• SVETKA, a program for multiple sequence alignments analysis
• ETS sequence conservation

SVETKA, a program for Analysis of Multiple Sequence Alignments . ... Analyse your alignment . ... Alignment . Nota Bene! .aln or .fasta format required!! Look here for comments . ... Nota Bene! Special scheme format required! ... Development of the program is supported by Ministry of Education and Science of the Russian Federation (State Contract No. ...

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• Geometrical core
• S : rm_systems
• Example of alignment

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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• Lathrop R.H., Rogers Jr R.G., Smith T.F. - A Bayes-optimal sequence-structure
• Brown S.M. - Bioinformatics: A Biologist's Guide to Biocomputing and the
• Korf I., Yandell M., Bedell J. - Blast (Basic Local Alignment Search Tool) ::

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/2015/proceedings/abstracts/164.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/66.pdf

... О UNИX . ... HelpOnTables . ... Table Markup . ... General table layout and HTML like options . ... Line breaks within cells . ... Bulleted lists and other complex content within cells To create a table, start & end a new line using the table marker; two 'pipe' characters " || ... top left cell || top right cell || || bottom left cell || bottom right cell || ... Just use CSS-formatted styles and it will be inlined in the generated HTML tag. <style="..."> will put that style info into cell (td) html ...

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• WikiCourse/15 Tables - UNИX

... О UNИX . ... HelpOnTables . ... Table Markup . ... General table layout and HTML like options . ... Line breaks within cells . ... Bulleted lists and other complex content within cells To create a table, start & end a new line using the table marker; two 'pipe' characters " || ... top left cell || top right cell || || bottom left cell || bottom right cell || ... Just use CSS-formatted styles and it will be inlined in the generated HTML tag. <style="..."> will put that style info into cell (td) html ...

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• WikiCourse/15 Tables - UNИX

... Class . ... Nested classes inherited from class javax.swing.JApplet . ... private int . ... private java.lang.String[] . ... private static int . ... Fields inherited from class javax.swing.JApplet . ... Fields inherited from class java.applet.Applet . Fields inherited