... 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: allpy/rna.py annotate
• allpy: allpy/dna.py annotate
• allpy: test/test.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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• Geometrical core
• SVETKA, a program for multiple sequence alignments analysis

... 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

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
• OUTPUT
• GeneBee

... 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

... annotate . ... ksenia_yashina@8 . ... 6 def __init__ ( self , delay = 10 , diam = 300 , num = 1 , env = 1 , reprod_a = False , reprod_s = False , life = 1 ): . ... 7 self . ... 15 def __repr__ ( self ): . ... 16 return "< %s , %s , %s , %s , %s , %s , %s >" % ( self . delay , self . diam , self . ... config ( text = "Stop" , command = self . ... config ( height = self . ... grid ( row = 0 , column = 2 , rowspan = 6 , padx = 50 , pady = 10 ) . ... config ( text = "Submit" , command = self . ...

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• petri_dish: Bacteria.py annotate
• petri_dish: Petri.py annotate

... 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

... Second, alignment of highly similar genomic sequences is useful for comparison of genome assemblies of the same organism or closely related ones. ... Nucleotide pangenome (NPG) of an input set of genomes is a set of aligned blocks, each block composed of orthologous fragments. ... Hemi-stable blocks (h-blocks) include no more than one fragment of a genome and lack a fragment of at least one of genomes. ... Blocks with repeats (r-blocks) include more than one fragment from one or several genomes. ...

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• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/161.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/156.pdf

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) ::

... Download Russian Journal of Biological Invasions, 2011, issue ? ... The second issue of the Russian Journal of Biological Invasions, 2011, presents 13 articles, in which the questions on introduction and dispersion of alien species in Russian regions and adjacent territories are considered. ... Web-site of Russian Journal of Biological Invasions is developed and supported by the . Group of Bioinformatics and Modeling Biological Processes" IPEE RAS . ... Russian Journal of Biological Invasions . ...

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• Russian Journal of Biological Invasions: 2010, issue ? 3
• Russian Journal of Biological Invasions: 2011, issue ? 1
• Russian Journal of Biological Invasions: 2011, issue ? 3

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

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

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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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... 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)
• Seminars
• Post main sequence stars (stage II)

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
• Research

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

... 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):
• An annotated checklist of the insectivores (Mammalia, Lipotyphla) of Vietnam

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"
• Efficiency of ARM processors for classical molecular dynamics

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
• http://storage.bioinf.fbb.msu.ru/~roman/mol_biol_mosk_2006.pdf
• http://storage.bioinf.fbb.msu.ru/~roman/batmas30.pdf

... The main interest of researchers was focused on TiO2:Co and TiO2:V thin films, that reveal an essential difference in their behavior: TiO2:Co films demonstrate either strong magnetization, MO response or AHE independently on presence or absence of magnetic Co clusters inside the films. ... It has been found that: thin films TiO2:Co(0.5%, 1.3% and 5%) have either magnetization or MO signal of Transversal Kerr effect with the absence of magnetic clusters. ...

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