... annotate . ... Changed the way related types are stored for Alignment, Block, Sequence, Monomer Now each of them has attribute 'type', which is an object with four attributes: - Alignment - Block - Sequence - Monomer . ... 1 import sys . bnagaev@83 . ... 3 from allpy.alignment import Alignment . ... 4 from allpy.block import Block . ... 6 p = Alignment ( open ( 'test.fasta' )) . ... 7 print "alignment length: %i " % len ( p ) . bnagaev@110 . ... bnagaev@120 . ... 13 b = Block ( p ) . ...

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• allpy: allpy/rna.py annotate
• allpy: allpy/dna.py annotate
• allpy: allpy/util.py annotate

The files containing information about Affymetrix microarrays were downloaded from the official Affymetrix site. ... Probe sequences were mapped to the genome using Blat. ... The hits found "probe alignment regions" were . ... We annotated each probe alignment region using the mRNA and EST alignments provided by UCSC, considering only . ... The textual part of the interface consists of probe information section, probe alignment section and transcription state . ... Each gene and each probe alignment . ...

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• SVETKA, a program for multiple sequence alignments analysis
• Geometrical core

S .. ... a database of structures of DNA-protein and RNA-protein complexes. ... a program for finding hydrophobic clusters in 3D structures of macromolecules . ... search of conserved hydrophobic clusters in aligned 3D structures of protein families . ... a program for analysis of multiple alignments . ... a program for automatic detection of aligned blocks in a multiple protein alignment. ... a program for detection of aligned blocks in a multiple alignment of sequences of PDB chains. ...

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• SVETKA, a program for multiple sequence alignments analysus
• SVETKA, a program for multiple sequence alignments analysis
• About this project

Home page . ... GeneBee . ... A4 - Genebee Adaptive Automated Annotation . ... Home . Advanced query . Annotation title . ... ITA[1,1] ITA[0,1] USUAL . Additional output . ... NRAS_1 MTEYKLVVVG AGGVGKSALT IQLIQNHFVD EYDPTIEDSY RKQVVIDGET CLLDILDTAG QEEYSAMRDQ VFAINNSKSF ADINLYREQI KRVKDSDDVP MVLVGNKCDL PTRTVDTKQA HELAKSYGIP GVEDAFYTLV REIRQYRMKK LNSSDDGTQG CMGLPCVVM . ... Last updated: December 23, 2008. ...

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• Genebee Predicted Annotation - Advanced
• GeneBee
• Genebee Predicted Annotation Help

... High-scoring Sequences . ... The E-value of a sequence is the expected number of sequences in a random database of the same size that would match the motifs as well as the sequence does and is equal to the combined p-value of the sequence times the number of sequences in the database. ... The score for the match of a position in a sequence to a motif is computed by by summing the appropriate entry from each column of the position-dependent scoring matrix that represents the motif. ... Sequence Name ...

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• Task 9 (sequence annotation)
• Global and Local Alignment of A.A Sequences

... Query: E. coli K12 tRNA (valV, selC, asnV, leuT, argZ from EMBL entry U00096 ) . ... BLASTN (both) | ... Nhunt . ... BLASTN (optimal): 3.5 s . BLASTN (default): 0.8 s . ... Nhunt: 7 s The program Nhunt surpass all other tested programs in sensitivity. ... Nhunt BLASTN (optimal): 2.9 s . ... Nhunt: 3.7 s BLASTN with default parameters actually cannot find any significant homologues. ... Nhunt-3: 1.7 s BLASTN with default parameters actually cann't find any significant homologues. ...

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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
• Brown S.M. - Bioinformatics: A Biologist's Guide to Biocomputing and the
• Abrams B., Abrams T. - .NET Framework Standard Library Annotated Reference

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/179.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

RnaViz . RnaViz is a user-friendly, portable, windows-type program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure can be changed easily. ... Home Site: . http://rrna.uia.ac.be/rnaviz/ . ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ... SAL@KachinaTech.COM . ...

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• SAL- Other Scientific Fields - Chemistry, Biology Related - Evalign
• SAL- Other Scientific Fields - Chemistry, Biology Related - PomBase
• SAL- Other Scientific Fields - Chemistry, Biology Related - DCSE

Key-words: rhythm, stress, syllable, rhythmic structure, syntagm, utterance, prosody, speech production, speech perception . ... In speech communication, RS are both units of speech production and speech perception. ... The research of speech rhythm in diachrony and synchrony consists of the analysis and the description of speech rhythmic units concerning Old Church Slavonic, Old Russian, Old High German in diachrony and Modern Russian, German, Czech and Bulgarian in synchrony. ...

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SCIENTIFIC TASKS AND RESULTS . In the results of searching for new perspective solid state materials for the quantum electronics, non-linear optics and other fields of physics more than 200 various oxide compounds were synthesized and peculiarities of their atomic structure and physical properties are studied. Single crystals of 80 such the compounds are grown and thoroughly investigated. ... A family of oxide-ion conductors on the base of La 2 Mo 2 O 9 (30.10.09) . ... Main page ...

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• Seminar in Polymer Physics

Roman Sutormin rsutormin@gmail.com Professional experience 05/2013 ­ present: Lawrence Berkeley National Laboratory (Berkeley, CA, USA) Software developer Development of JSON based storage system used for keeping biological data involved in public KBase services. ... 10/2009 ­ 08/2011: Mail.Ru Group (Moscow, Russia), Software developer Support and development of data warehouse (PostgreSQL) and administration web tool (JBoss + GWT) on serverside of MMO game "Allods Online". ... 2013 Jul 1514(1):476. ...

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• http://storage.bioinf.fbb.msu.ru/~roman/Sutormin_CV_aug2013.pdf

... An annotated checklist of 32 extant species from 12 genera of the insectivores (Mammalia, Lipotyphla) of Vietnam is provided. ... Литература Скачать PDF . A preliminary study on genetic divergence of the Asian lesser white-toothed shrew Crocidura shantungensis (Mammalia: Soricomorpha) in mainland Korea, adjacent islands and continental East Asia: cytochrome b sequence analysis . ... Musk deer Moschus moschiferus nutrition in the Tukuringra Mountain Range, Russian Far East, during the snow season . ...

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• Contribution to the species composition and taxonomic status of some Rattus
• An annotated checklist of the insectivores (Mammalia, Lipotyphla) of Vietnam
• Geographical pattern and historical demography of Midday gerbil Meriones

under the terms of the GNU General Public License v2 # $Id$ EAPI= 5 inherit perl-module DESCRIPTION= Do It Yourself Annotation , a collection of tools and libraries for sequence assembly and annotation HOMEPAGE= http ://gmod.org/wiki/ Diya SRC_URI= mirror://sourceforge/diyg/files/ diya / diya -1.0/ S="${WORKDIR}/diya-${PV/_/-}" SRC_TEST=do src_install() { mydoc="INSTALL README docs/diya.html" perl-module_src_install insinto /usr/share/${PN} doins -r diya.conf docs examples scripts } ...

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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/rfc-editor/rfc-ed-all/rfc4304.txt

... 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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• Attributes | PARALLEL.RU - Информационно-аналитический центр по параллельным

... 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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• Alignment, font styles, and horizontal rules in HTML documents
• Basic HTML data types
• Index of the HTML 4.0 Attributes

... HTML defines six levels of headings. ... The numbering style is controlled by the style sheet, e.g. The style sheet specifies whether headers are numbered, and which style is used to render the current sequence number, e.g. arabic, upper alpha, lower alpha, upper roman, lower roman or a numbering scheme appropriate to the current language. ... CLEAR . ... This attribute is used to set the sequence number associated with the header level of the current element to a given number, e.g. SEQNUM=10. ...

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• Ordered Lists
• List Item
• Table Rows

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

. Выберите категорию обращения: Общие вопросы Отчеты Рейтинги Диссертационные советы Конкурсы Ввод данных Структура организаций Пользователи Проблемы с регистрацией\входом в систему . Тема обращения: . Описание проблемы: . Введите почтовый адрес: . Войти в систему . Регистрация . Главная . Поиск . Статистика . О проекте . Помощь . Издательство: Taylor & Francis . Местоположение издательства: United Kingdom . ї 2011-2015 НИИ механики МГУ . Лаборатория 404. Все права защищены. обратная связь . Создать

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• Journal of Integer Sequences - журнал | ИСТИНА - Интеллектуальная Система
• METHOD FOR SIMULTANEOUSLY DETECTING A PLURALITY OF RNA SEQUENCES IN A
• Protein sequences & data analysis - журнал | ИСТИНА - Интеллектуальная Система