... 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

... 2 from allpy import protein . ... 5 # Create sequences from string representation of sequence body . 6 sequence_1 = protein . ... 9 # Create alignment from sequences . 10 alignment = protein . ... 15 # For each sequence, print number of gaps and non-gaps in alignment . ... 19 for column in alignment . ... 24 print " %s : %s gaps, %s non-gaps" % ( row . ... 26 # Print number of gaps in each column . ... 29 column_gaps = 0 . 30 for sequence in alignment . ... 31 if sequence not in column : . ...

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• allpy: 73070c394dc4 allpy/fileio.py
• allpy: b2ec17578145 lib/block.py
• allpy: fb3164f03984 lib/block.py

... Both sequences must be either nucleotides or proteins. ... For blastx 1st argument should be nucleotide [String] default = blastp -g Gapped [T/F] default = T -o alignment output file [ File Out] default = stdout -d theor. db size ( zero is real size) [ Integer ] default = 0 -a SeqAnnot output file [ File Out] Optional -G Cost to open a gap ( zero invokes default behavior ) [ Integer ] default = 0 -E Cost to extend a gap ( zero invokes ...

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• http://kodomo.cmm.msu.ru/~vasilisa/fdnaml_help.txt
• Global and Local Alignment of A.A Sequences
• Множественное выравнивание.

Электронная библиотека Попечительского совета . ... Narkiewicz W. - Uniform Distribution Of Sequences Of Integers In Residue Classes . ... Название: Uniform Distribution Of Sequences Of Integers In Residue Classes . Автор: Narkiewicz W. Язык: . ... Sequence uniformly distributed mod N 1 . Sequence weakly uniformly distributed mod N 8 . ... Uniform distribution mod N 1 . Uniform distribution mod N, criterion 1 . ... Электронная библиотека попечительского совета мехмата МГУ , 2004-2016 . ...

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• Sloane N.J.A., Plouffe S. - The Encyclopedia of Integer Sequences ::
• 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

... Войти в систему . ... Blasiak P., Dattoli G. , Horzela A. , Penson K.A., Zhukovsky K. в журнале Journal of Integer Sequences , издательство University of Waterloo (Canada) , том 11, с. 1-11 . ... Kolpakov R. в журнале Journal of Integer Sequences , издательство University of Waterloo (Canada) , том 10, ? ... в журнале Journal of Integer Sequences , издательство University of Waterloo (Canada) , том 5, ? ...

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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

. SVETKA, a program for Analysis of Multiple Sequence Alignments . Helps (useful info) . Analyse your alignment . Interesting . links . Our Country . loads for a long time! . Our City . Our University . Our Institute . Our seminar . Our project . Name (optional) . Alignment . Nota Bene! .aln or .fasta format required!!! . Look here for comments . Tree (optional) . Nota Bene! Special scheme format required! . Look here for comments .

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• SVETKA, a program for multiple sequence alignments analysis
• ETS sequence conservation
• Inquiry information || Rule of four sequences

... 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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• Lower-bound and upper-bound markers | PARALLEL.RU - Информационно-аналитический

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/4.pdf

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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• Input Formats
• SDPpred
• SDPsite - Algorithm Format requirements

... Peptide Sequence Databases . ... BLAST searches can be limited to the results of an Entrez query against the database chosen. ... For example: Mus musculus[Organism] For help in constructing Entrez queries please see the " Writing Advanced Search Statements " section of the Entrez Help document. ... Only following combinations of the Matrix, Open & Extended Gaps are available: Recomended combinations are colored. ... Gap . ... Standard BLAST alignment in pairs of query sequence and database match. ...

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• GeneBee BLAST 2.2.22+ Services Help
• AliGraf - GeneBee Graphical Alignment Help
• AliComp - GeneBee Alignment Comparison Help

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

... TWikiMetaData . ... Meta Data Syntax . ... META:FORM . ... Additional topic data, program-generated or from TWikiForms , is stored in META variable name/value pairs . TWikiMetaData uses META variables to store topic data that's separate from the main free-form content. ... Use META variables to format and display Meta Data. Format is the same as in TWikiVariables , except all fields have a key. ... Note: Please contribute updates to this topic on TWiki.org at TWiki:TWiki.TWikiMetaData . ...

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• TWikiMetaData - TWiki - TWiki - (printable)

Используя базовые типы и применяя небольшой набор способов построения, можно получать сложные типы. ... Получаемые в результате типы называют структурированными. В ASN.1 определяется шесть способов структурирования: "последовательность" (SEQUENCE), "последовательность из" (SEQUENCE OF), "множество" (SET), "множество из" (SET OF), выборочный тип (CHOICE), селективный тип. ... Селективный тип - это структурированный тип, определяемый указанием одного из типов-компонентов выборочного типа. ...

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• Часть XIII - Пример описания ASN.1
• Integers
• range

... CROSSBOW Definition 4.1 CROSSBOW Group OBJECT : fmxHubHwVer { fmxSystemGrp 1 } Syntax : OCTET STRING Definition : Access : read-only Status : mandatory OBJECT : fmxHubFwVer { fmxSystemGrp 2 } Syntax : OCTET STRING Definition : Access : read-only Status : mandatory OBJECT : fmxHubAddress { fmxSystemGrp 3 } Syntax : OCTET STRING Definition : Access : read-only ...

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• http://mirror.msu.net/pub/gentoo-portage/sci-biology/mafft/mafft-7.050.ebuild
• http://mirror.msu.net/pub/gentoo-portage/sci-biology/mafft/mafft-7.215.ebuild
• http://mirror.msu.net/pub/slackware-current/slackware/l/qjson-0.8.1-i486-1.txt

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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... Поступление в лабораторию . ... Электронный журнал "Компьютерная графика и мультимедиа" . ... MSU Graphics & Media Lab (Video Group) . The algorithm allows to increase video frame rate (fps) by the factor equal to any integer number. ... Frame rate conversion is done as shown on the picture below: . Frame rate conversion scheme . ... arbitrary whole number of interpolated frames between reference frames. ... Previous reference frame . ... Video Frame Rate Double Up-Conversion . ...

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• Video Frame Rate N-Times Up-Conversion | Graphics and Media Lab
• x264 codec improvement | Graphics and Media Lab
• Novel Approach for Video Codecs Scoring using Specially Prepared Video

... A regular expression (regex) is a powerful way of specifying a complex search. MySQL uses regular Henry Spencer's inplementation of regular expressions. ... MySQL uses the extended version. This is a simplistic reference that skips the details. To get more exact information, see Henry Spencer's regex(7) manual page that is included in the source distribution. ... A regular expression describes a set of strings. The simplest regexp is one that has no special characters in it. ...

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• Be Paranoid-- Call Sequence Checks

Next: Roche lobe overflow (stage Up: Principal Evolutionary States of Previous: Main-sequence stars (stage I) . ... The duration of this stage for a binary component is no longer a function of the stellar mass alone (as in the case of single stars), but also depends on the initial binary type (A, B or C) (Iben and Tutukov, 1985, 1987[ 74 , 75 ]): . The radius of the post-MS star rapidly increases (on a thermal time-scale)   and reaches characteristic giant values. ...

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• Main-sequence stars (stage I)

Astronomy Picture of the Day . La Palma Eclipse Sequence . ... Credit Copyright: Miguel Claro ( TWAN ) Explanation: At left, a dramatic image sequence follows late September's total lunar eclipse above a rugged landscape and sea of clouds from the Canary island of La Palma . Composited in a circular fisheye projection, the brightness of the Full Perigee Moon changes drastically in transition from outside the total eclipse phase compared to its dim glow during the 72 minute long totality . ...

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• Bakasa Eclipse Sequence
• Alaska Aurora Sequence
• Астронет > Bakasa Eclipse Sequence