237deca179632c4284df36ab098b76dc64b116fa # Parent 88631907f23daf178438cf9313ab1af0ed6f449d Converted docstrings and init of base. Block to match our plan diff -r 88631907f23d -r 237deca17963 allpy /base.py --- a/ allpy /base.py Thu Dec 16 19:24:22 2010 +0300 +++ b/ allpy /base.py Thu Dec 16 20:42:42 2010 +0300 @@ -336,43 +336,43 @@ pass - ## Unclean code follows +class Block (object): + Block of alignment . -class ... If sequences are not given, the block uses all sequences in alignment. ...

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• allpy: allpy/base.py diff
• allpy: 45573ee48844
• allpy: 20636c0df58c

... 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
• Input Formats
• SDPpred

... 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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... Parsimony method . ... It is based on the following principle: the ancestral sequences (posed in nodes of a phylogenetic tree) should be such that the minimal required number of character replacements on the branches of the tree is less than for any other choice of sequences. ... If the preliminary character of the node is * , but the output character of its immediate ancestor is some letter (say, X ), and its set of possible characters contains X , then the output character of the node is also X . ...

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• Inquiry information || Distances
• SDP home page
• About this project

AliComp - GeneBee Alignment Comparison Help Type in a title for this session for you to remember. ... First alignment: .* ... HCVPCP2 ( 279) LLSVTSVVM------VGGYVAPVNTVKPKPVINQ TGVPCP2 ( 277) AIASNFVVKK-PQAEERPKNCAFNKVAASPKIVQ MHVPCP2 ( 288) CLYLKNLKQTFSSVLTTFYLDDVKCVEYKPDLSQ MHVPCP1 ( 272) GYGMTFSMSPFELAQLYGSCITPNVCFVK----- HCVPCP1 ( 262) TICIKDADY---NAKVEISVTPIKN--------- TGVPCP1 ( 256) TLFINANVM--TRAEKPKQEFKVEKVEQQPIVEE IBVPCP ( 282) AMYTRFAFK----NETSLPVAKQSKGKSKS-VKE Second alignment : ...

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... Alternative core new atoms (%) . ... An alignment of a set of structures is a set of positions , to each position some atoms from different structures correspond. ... Geometrical core of a set of structures is a subset of alignment positions those atoms are disposed similarly in all structures. ... For any two positions included into geometrical core, the distances between CA atoms of those positions in all structures may differ not more than the value of the parameter "Distance spreading". ...

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Detection of short size mutations and copy number alterations in ultra-deep targeted sequencing data Valentina Boeva, Emmanuel Barillot, Institut Curie, valentina.boeva@curie.fr Jean-Francois Laes OncoDNA, jf.laes@oncodna.com The emergence of the amplicon sequencing technique, which followed whole exome sequencing, promises a revolution in cancer diagnostics and treatment. ... Visualization of the typical configuration of read mappings (with Integrative Genomics Viewer). ...

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• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/136.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/244.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/4.pdf

... Minimal size of Clud clusters (residues) . ... An alignment of a set of structures is a set of positions , to each position some atoms from different structures correspond. ... Hydrophobic cluster of a single protein structure is a separated pool of nonpolar atoms. Usually there is the biggest cluster in the protein called hydrophobic core. ... ConClus program is able to detect of conservative hydrophobic clusters for a family of related protein domains or just for a set of aligned proteins. ...

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... The first column gives the star identification number, followed by X, Y positions in mm. The zero point of these offsets is star number 1 which lies at 21:24:20.52 +36:30:25.6 (equator and equinox 2000). Next are relative proper motions (muX and muY) and their errors (ex and ey) in 10**4 arcsec/yr, followed by calculated V magnitudes. The final column gives the calculated membership probabilities in percent. ...

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• SAL- Other Scientific Fields - Chemistry, Biology Related - Evalign
• APOD: 2015 October 7 - La Palma Eclipse Sequence
• APOD: 2001 July 6 - Bakasa Eclipse Sequence

. Next: Initial velocity Up: Space and velocity distributions Previous: Space and velocity distributions . Following Paczynsky (1990), we assume initial space distribution of young neutron stars to be varying exponentially with distance from the Galactic center and from the Galactic plane, that is probability distribution for young neutron star positions can be written in the form . with kpc, and pc. Mike E. Prokhorov . Fri Jul 19 19:16:07 MSD 1996

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This diagram illustrates the effects of absolutely positioning a box ("inner") with respect to a containing block established by a relatively positioned ancestor ("outer"). ... The "inner" box has been positioned relative to the top and left edges of the "outer" element's first inline box. ... The reference edges for positioning the "inner" box are indicated in the diagram by thick dashed lines. ... 1 Beginning of body contents.| ... 4 [(+200, -100)] 5 Inner 6 contents. ... Inner contents" is blue. ...

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• Dynamic HTML in Communicator
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• Long description for example illustrating absolute positioning

... 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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• Writing wrapper definitions | PARALLEL.RU - Информационно-аналитический центр

You can also sort on a specific part of a field if necessary. To define which part of a field to sort on you give the position in the field at which to start the sort followed by the position in the field at which to end the sort. The position at which to start the sort is given as the number of fields to skip followed by the number of characters to skip. ... tells sort to skip the first two fields and the first three characters of field 3. ...

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Astronomy Picture of the Day . ... Credit Copyright: Cenk E. Tezel and Tun Tezel ( TWAN ) Explanation: If you went outside at exactly the same time every day and took a picture that included the Sun, how would the Sun's position change? ... Yesterday, the Winter Solstice day in Earth's northern hemisphere, the Sun appeared at the bottom of the analemma. ... Pictured is such a total solar eclipse analemma or Tutulemma - a term coined by the photographers based on the Turkish word for eclipse. ...

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... Форумы > Аспирантура > Тема . ... Форумы Список тем Новая тема . ... Позиция постдока в Университете Бергена, Норвегия, прикладная математика, 4 года . ... Извините, только зарегистрированные пользователи могут публиковать сообщения в этом форуме. ... Сайт работает с 29.08.2000, Copyright 2000 2011 MMOnline.Ru and MMForce.Net, . ...

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• MMOnline | Форумы | Аспирантура | Аспирантура в Барселоне, 15тыс евро в год,
• MMOnline | Форумы | Аспирантура | PhD position in the University of Florida
• MMOnline | Форумы | Аспирантура | PhD positions in logic and AI, Vancouver

Электронная библиотека Попечительского совета . ... Bao-Yen Tsui J. - Fundamentals of Global Positioning System Receivers: A Software Approach . ... Название: Fundamentals of Global Positioning System Receivers: A Software Approach . Автор: Bao-Yen Tsui J. Аннотация: . ... The Second Edition of this acclaimed publication enables readers to understand and apply the complex operation principles of global positioning system (GPS) receivers. ... GPS receiver related subjects . ...

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PHP Manual . ... PHP 3 <= 3.0.18, PHP 4 >= 4.0.0) fseek -- Seeks on a file pointer . int fseek ( int fp, int offset [, int whence]) . Sets the file position indicator for the file referenced by fp .The new position, measured in bytes from the beginning of the file, is obtained by adding offset to the position specified by whence , whose values are defined as follows: . SEEK_SET - Set position equal to offset bytes. ... SEEK_END - Set position to end-of-file plus offset . ...

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... Give an example of chemical reaction between a salt and an acid leading to the formation of another salt and a base. (1 point) [Solution] . ... Write the reactions of chromium (III) bromide with hydrogen peroxide in acidic and basic media. (2 points) [Solution] . ... In the reactions, specify the structures of all substances. (3 points) [Solution] . ... Three substances A, B, and C were mixed in the amount of three moles each. ... Example problems in chemistry for the entrance exams ( main round ) ....

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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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... As a point of departure consider Russian data, where nouns denoting male individuals are always masculine (1a), while nouns denoting female individuals are always feminine (1b). (1) a. xorСs-ij good-MASC.N. `good father' SG ot'Иc father.N. SG (MASC b. xorСs-aja ) good-FEM.N.SG `good mother' mАt' mother.N. SG (FEM ) Thus, we can predict grammatical gender of a noun (`masculine' or ` feminine') on the basis of its semantics (`male' or `female') (Corbett 1991). ... Halkomelem lacks n-GENDER. ...

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