... 1 from allpy import protein . ... 3 # Create sequences from string representation of sequence body . 4 sequence_1 = protein . ... 7 # Create alignment from sequences . 8 alignment = protein . ... 13 # For each sequence, print number of gaps and non-gaps in alignment . ... 17 for column in alignment . ... 22 print " %s : %s gaps, %s non-gaps" % ( row . ... 24 # Print number of gaps in each column . ... 27 column_gaps = 0 . 28 for sequence in alignment . ... 29 if sequence not in column : . ...

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• allpy: lib/block.py annotate
• allpy: 6c4dc940fcdf test/usecase1.py
• allpy: NEWS 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

... 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

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
• ETS sequence conservation

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 - GeneMine
• SAL- Other Scientific Fields - Chemistry, Biology Related - MODELLER

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 BLAST 2.2.22+ Services Help
• GeneBee BLAST 2.2.8 Services 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. ... Sequence Name . ... Following the description line(s) is a line giving the length, combined p-value, and E-value of the sequence as defined in Section I. The next line reproduces the motif diagram from Section II. ...

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

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/197.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/161.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/164.pdf

Welcome , Registration , and other StartingPoints ; TWiki history & Wiki style; All the docs.. ... WikiNotation 2 - 1999-12-14 - PeterThoeny . ... TWiki is linking topics automatically, provided you give a WikiTopic a name that follows the WikiNotation . ... TWiki links topics automatically, provided you give a WikiTopic a name that follows the WikiNotation . ... Uppercase letter(s) . Lowercase letter(s) . ... Note: Please contribute updates to this topic on TWiki.org at TWiki:TWiki.WikiNotation . ...

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• %TOPICTITLE% (2 vs. 3) - TWiki
• WikiNotation - TWiki - TWiki
• %TOPICTITLE% (6 vs. 7) - TWiki

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
• SDPlight
• SDPpred

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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. Please standby and you will be automatically connected to the new location of the unframed Supernova page. Or, click on the link above. If you have questions or problems, please email me at David Bishop dbishop@vhdl.org . Last modified: Mon Aug 27 12:40:15 EDT 2001

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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

You can search database for submitted information. ... Character * specifies arbitrary character sequence (eg. '*n' will result: John, Martin etc.) Character * is placed at end of line automatically ('Mar*' = 'Mar' will result: Martin, Martina etc.) Blank form will result ALL database records. ... Family name: . ... Topic: . ... Seismo-tectonics of Tsunami 3. Numerical and Analytical Models of Local Tsunami Behavior 4. ... Recent Local Tsunamis 8. ... Information . ... Database search . ...

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... 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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• An annotated checklist of the insectivores (Mammalia, Lipotyphla) of Vietnam
• Geographical pattern and historical demography of Midday gerbil Meriones
• DNA polymorphism within Sorex araneus from European Russia as inferred from

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/media-video/pgmfindclip/pgmfindclip-1.13.ebuild
• 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

... 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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• Creating logfiles | PARALLEL.RU - Информационно-аналитический центр по

... About lab . ... Online Journal "Computer graphics and multimedia" (in russian) . ... Temporal Post-processing Method for Automatically Generated Depth Maps . ...

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