... sequence_based_blocks_search/blocks_finder.py . ... 1.1 --- a/ sequence _based_blocks_search/blocks_finder.py Fri Mar 23 01:34:48 2012 +0400 1.2 +++ b/ sequence _based_blocks_search/blocks_finder.py Mon Mar 26 22:08:08 2012 +0400 1.3 @@ -4,10 +4,47 @@ 1.4 sys.path.append( ../ ) 1.5 from allpy import protein 1.6 from allpy .homology import * 1.7 +from allpy import data 1.8 +from allpy import base 1.9 import copy 1.10 import math 1.11 from functional_groups ...

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• allpy: 7477ef0120e1
• allpy: 027f0f2f5417
• allpy: 116f5bfc39b8

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

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.

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
• Example of alignment
• S : rm_systems

... 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

... 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
• Nhunt

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
• Korf I., Yandell M., Bedell J. - Blast (Basic Local Alignment Search Tool) ::
• Brown S.M. - Bioinformatics: A Biologist's Guide to Biocomputing and the

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/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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• SAL- Other Scientific Fields - Chemistry, Biology Related - DCSE
• SAL- Other Scientific Fields - Chemistry, Biology Related - ClustalW
• SAL- Other Scientific Fields - Chemistry, Biology Related - HMMER

... Cell border width (pixels). unspecified . ... Column to sort initially ( "1" to number of columns). unspecified . ... Data cell alignment, one value for all columns, or a comma separated list for different alignment of individual columns. ... Data cell background colour of a sorted column; see databg . ... Data cell text colour, a comma separated list. unspecified . ... Header cell alignment, one value for all columns, or a comma separated list for different alignment of individual columns. ...

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

Изучение статистики наиболее длинной общей подпослеовательности двух случайных подпоследовательностей является одной из самых интересных и трудных задач вычислительной математической биологии. В докладе будут представлены результаты, касающиеся статистического распределения