... Columns represented with one sequence or pure gap columns are not considered. Calculate weighted average of number of connected components in columns. Weight of column = l / sum(l) (l = number of sequnces representing column) . ... 9 # Create alignment from sequences . ... 15 # For each sequence, print number of gaps and non-gaps in alignment . ... 19 for column in alignment . ... 26 # Print number of gaps in each column . ... 29 column_gaps = 0 . ... 31 if sequence not in column : . ...

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• allpy: 2ede0318ff95 test/usecase1.py
• allpy: ee2c10aa74b8
• allpy: 2ede0318ff95 allpy/protein.py

... Distances between sequences . It is considered that the space, where all amino acids and sequences are analysed, is a metric one. ... When the distance between amino acids is entered, it is rather easy to consider such measure as pair distance between sequences in any position of alignment (in fact, this distance is just a distance between two amino acids). As distance is an additional quantity, pair distance between sequences on all alignment positions can be easily defined. ...

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• Inquiry information || Rule of four sequences
• About this project
• About authors ot this complex

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
• PLANdbAffy: probe-level annotation database for Affymetrix expression

... 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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• SDPlight
• RNA Alignment
• Input Formats

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/156.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/161.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/164.pdf

... Instructions are in README.TXT file inside the tarball. ... tar -xvf nhunt_x86.tar Query and database files should contain sequences in FASTA format ( wikipedia description ). ... Default name of the output file is 'nhunt.out'. ... Any parameter consists of key and value and is called as '-key value', where 'key' is one character and 'value' is any number of characters. -i Query file . ... No default value. -d Database file . ... No default value. -o Output file . ... Default value: 'nhunt.out' . ...

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• ConClus
• Nhunt

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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• Changeset 120:a8549a69f959 тАУ Python Battle
• Множественное выравнивание.
• Changeset 63:27a43636ab6e тАУ Python Battle

... Submitted Sequences: . ... Results 1.REFINED ALIGNMENT Power 4.27 Homology percent 5.3 Symbols used in the alighnment charts: ' ' - average weight of column pair exchanges is less than weight matrix mean value '.' - is less than mean value plus one SD '+' - is less than mean value plus two SD '*' - is greater than mean value plus two SD .. ... SQ1 ( 48) yhtcggillnSHWVLTAAHCFKNKkkvt SQ2 ( 46) srqtfsirsiSQNGYDPRQNLNDVL--- SQ3 ( 1) ----------SRRTYTLTDYLKSTFr-- 5TH LOCAL SUPERMOTIF, power 2.51 + *.. ...

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• RNA secondary structure prediction
• AliGraf - GeneBee Graphical Alignment Help
• AliComp - GeneBee Alignment Comparison Help

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) ::

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

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

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... The evolution of a binary system is considered as a sequence of stages the duration of which are defined by the shortest evolutionary time-scale of one of the binary components (see the list of the evolutionary states of stars in Sections 3 and 4). ... Then the code finds a new stage the binary should transit to, with this stage being determined by the evolutionary states of both components, and calculates it. ... However, one can use the algorithm described above to model their evolution. ...

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• Main-sequence stars (stage I)
• Post main sequence stars (stage II)
• Initial parameters of compact stars

Jupiter and Saturn Pas de Deux . ... Credit Copyright: Tunc Tezel Explanation: Viewed from Earth, the solar system's planets do a cosmic dance that is hard to appreciate on any single night. ... It reveals the graceful looping or retrograde motion of bright wanderers Jupiter (leftmost) and Saturn. ... Retrograde motion can be seen each time Earth overtakes and laps planets orbiting farther from the Sun, Earth moving more rapidly through its own relatively close-in orbit. ... NASA Official: Jay Norris. ...

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• Jupiter and Saturn Pas de Deux
• Астронет > Jupiter and Saturn Pas de Deux
• La Palma Eclipse Sequence

Enclosure structures of equal level line fields in the gradient filling problem" . Ivanov B.N. In this paper, the method of gradient filling of equal level line fields by color scale is considered. ... The root tree structure of equal level line enclosure is applied to the context analysis of all equal level line values in order to correctly specify the color values of their filling. A working algorithm of gradient filling of equal level lines is given. PostScript (in Russian) (2.67MB) . ...

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• "Mathematical simulation: principal segments, their peculiarities, and...
• "Routing on lattice-cellular structures"
• Iterative methods for solving inverse problems of ultrasonic tomography

... We obtained 20 complete cytochrome b sequences (1140 bp) of Meles leucurus from the Korean Peninsula (mainland Korea and Jeju Island), Russian Far East, and Mongolia, and these sequences were compared to complete and partial (629 bp) sequences of M. leucurus , obtained from GenBank, in order to reexamine genetic differentiation among M. leucurus from Korea, Siberian and Far-eastern Russia, Mongolia, and China. ...

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• Two sympatric phylogroups of the Asian badger Meles leucurus (Carnivora:
• The в??developmental conduitв?? of the tribe Microtini (Rodentia, Arvicolinae):
• Geographical pattern and historical demography of Midday gerbil Meriones

... Research programm of the laboratory-chair< . ... Laboratory-chair of Discrete mechanics on a microscopic scale . ... Thus the structures of the physical world are not physical objects but physical processes. ... The primitive entity is called a material point. ... The value of the property “existence” of the material point varies from “the material point does not exist” to “the material point exists” by this process. ... Let call this structure a dynamical graph or a d-graph. ...

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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 общих подпоследовательностей в упрощенном (некоррелированном) варианте модели, т.наз. модели Бернулли . ...

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• Research

... 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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• File Size | PARALLEL.RU - Информационно-аналитический центр по параллельным
• Progress | PARALLEL.RU - Информационно-аналитический центр по параллельным
• File Consistency | PARALLEL.RU - Информационно-аналитический центр по

... 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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... Кафедра общей экологии Биологического факультета МГУ им. М.В. Ломоносова и . ... Активные темы Список участников Поиск по форуму Помощь . ... Экологический Форум - Фундаментальная Экология : Предложения и замечания по сайту . Тема: Dyeing shoes is considered by some to be . ... Переход на форум -- Выберите форум -- О сайте "Фундаментальная экология" - Предложения и замечания по сайту Научные семинары - Научные семинары . Вы не можете публиковать новые темы в этом форуме . ...

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• Экологический Форум - Фундаментальная Экология: considered one of a form Radar
• Экологический Форум - Фундаментальная Экология: Brogues are considered top of
• Экологический Форум - Фундаментальная Экология: Mark non-essential. considered