... See #95 1) Sequences, Alignment and Blocks now have two new methods: - add_markup(name, markup_class=optional, **kwargs=optional) - remove_markup(name) name refers to the same name as in aln.markups[name] or sequence[i].name It is now explicitly denied to create markups any other way. ... For sequences markups it removes markup attribute from each monomer. 3) Added necessary del sequence_markup[monomer] method. ... add_markup ( name , markup_class = cls ) . ... 39 def to_record ( self ): . ...

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• allpy: 835efa2a8c71 allpy/markup.py
• allpy: bf873e4054c2 allpy/markups.py
• allpy: 3a712982ceb8 allpy/markups.py

... List of solitary restriction endonucleases in complete prokaryotic genomes . List of groups of orthologous R-M systems. List of all analyzed genomes. Contains those orthologous groups that include at least one separated R-M system . R-M orthologous group ID . REs alignments . MTases alignment . Group 1 . ...

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• Geometrical core

... All contacts alignment . ... Blue background means a contact with backbone phosphate. ... HBond with major groove + contact through a molecule of water with backbone phosphate; . ... contacts through water molecules both with backbone phosphate and major groove; . ... HBond with major groove + contacts through water molecules both with backbone phosphate and major groove; . ... HBond with major groove + engagement in hydrophobic cluster + contact through a molecule of water with backbone phosphate; ...

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• ETS numeration assumed
• HTH3_numeration_assumed
• Homeodomain numeration assumed

... 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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• Site Cluster
• SDPsite - PF07978
• SDPsite - PF01206

... Lathrop R.H., Rogers Jr R.G., Smith T.F. - A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment . ... Название: A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment . Авторы: Lathrop R.H., Rogers Jr R.G., Smith T.F. Аннотация: . A rigorous Bayesian analysis is presented that unifies protein sequence-structure alignment and recognition. ...

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• Heggins D., Taylor W. - Bioinformatics: Sequence, Structure and Databanks ::

... 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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• Nhunt: program for nucleic acid sequence similarity search

Sequence alignment of non-superposable beta-sheets Evgeniy Aksianov Belozersky Institute, Lomonosov Moscow State University, Leninskie Gori 1, Moscow, Russia, evaksianov@gmail.com Andrey V. Alexeevski Belozersky Institute, Lomonosov Moscow State University, Scientific Research Institute for System Studies (NIISI RAN), Moscow, Russia aba@belozersky.msu.ru Protein 3D structures usually are more conserved than their sequences. ... Beta-strands are contained in sheet map rows. ...

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• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/167.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/244.pdf

... 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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• Partitioning of Cartesian structures | PARALLEL.RU -
• MINLOC and MAXLOC | PARALLEL.RU - Информационно-аналитический центр по

... If there's no significant multiple alignment , including the sequence, that you interest, then the secondary structure is built, using only the energy model (just the potential energy of the system is minimized), but very often such method will give unreliable results. ... It should be mentioned that by default, at alignment case, the RNA secondary structure will be predicted for the first sequence of the alignment. ... It is done through optimizing, not the real, but model energy of the structure. ...

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• Bioinformatics portal, Moscow State University
• Databases
• INTAS :: Global and Local Protein Matching

Scoring Matrices . Matrix Sequences Sequence Consisting of the first four Amino Acids in the Protein GYRB_ECOL: . ... Sequence Achieved by Substitution of the 2nd and 4th Amino Acid and Insertion between the 3d and 4th Amino Acid, in the Protein GYRB_ECOLI, to randomly chosen new amino acids: . ... Matrix Sequences Sequence Consisting of the First Nine Amino Acids of the Protein GYRB_ECOLI: . ... Sequence Consisting of 2nd, 3d, 7th, 8th and 9th Amino Acid Residues of the Protein GYRB_ECOLI: . ...

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• Conservative Amino Acid Residues
• Structure Alignment
• статьи о карбоксилэстеразе bioH

... Sinergetic has recommended itself in the most various areas: to physics, chemistry, biology, and even in public sciences. ... The purpose of research was the study of laws of heat transfer process in active environment, which is nonequilibrium and itself can give the contribution to change of temperature. ...

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... Structure and properties of chimeric small heat shock proteins containing yellow fluorescent protein attached to their C-terminal ends. ... Recombinant chimeras of small heat shock proteins (sHsp) HspB1, HspB5, and HspB6 containing enhanced yellow fluorescent protein (EYFP) attached to their C-terminal ends were constructed and purified. Some properties of these chimeras were compared with the corresponding properties of the same chimeras containing EYFP attached to the N-terminal end of sHsp. ...

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• The role of intrinsically disordered regions in the structure and functioning
• Structure, properties, and functions of the human small heat-shock protein
• Effect of mutations in the beta5-beta7 loop on the structure and properties of

... The LanHEP input file is the sequence of statements, each starts with a special identifier (such as parameter, lterm etc) and ends with the full-stop ' . ... This section is aimed to clarify the syntax of LanHEP input files, i.e. the structure of the statements. ... Let us consider the LanHEP input files for the Standard Model with both the t'Hooft-Feynman and unitary gauges. ... LanHEP allows the user to define several keys , and use these keys to branch among several variants of the model. ...

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• C case

Home . Database of structures of nucleic acid - protein complexes . ... List of complexes . Pfam families . SCOP families . Interaction classes . ... NPIDB . ... Information on SCOP and Pfam domains detected in protein chains is presented. ... Each family has its own web page with the list of entries that include domains of the family. ... List of SCOP domains occurred in DNA-protein and RNA-protein complexes is organized in tree-like form, according to the SCOP classification. ...

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• NPIDB: 5DPK structure

This home page belongs to small group of scientists working at . Sternberg Astronomical Institute which is a part of Moscow State University . ... Электронная библиотека научно-технической и художественной литературы (доступна только из ГАИШ) . ... Local staff . Dr. Edward Kononovich (konon -at- sai.msu.ru), Associate Professor . ... Dr. Sergey Ayukov (asv -at- sai.msu.ru), Research Fellow, Webmaster of the group . ... Joint seminar of Solar Studies Structure Group and Solar Photometry Group . ...

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• Not so well documented Device Helpers in OS/2

... LDAP is the Lightweight Directory Access Protocol, and is a protocol used to access "Directory Servers". ... Search surname entry $sr= ldap _ search ($ds, o=My Company, c=US , sn=S* ); echo Search result is .$sr. p ; echo Number of entires returned is . ldap _count_ entries ($ds,$sr). p ; echo Getting entries ... p ; $info = ldap _ get _ entries ($ds, $sr); ... ldap_get_attributes -- Get attributes from a search result entry . ... ldap_get_entries -- Get all result entries...

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• Declaration of the Zend Module Block
• MCAL functions
• mcal_fetch_current_stream_event

... Global Ocean Suspected on Saturns Enceladus . ... 20.09.2015 . ... Credit Copyright: Cassini Imaging Team , SSI , JPL , ESA , NASA Explanation: Do some surface features on Enceladus roll like a conveyor belt? ... Inspection of these images show clear tectonic displacements where large portions of the surface all appear to move all in one direction. ... The small magnitude of Enceladus' wobble as it orbits Saturn might indicate damping by a globally extending underground ocean layer . ... 2015 2016 ....

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• Journal "Peremennye Zvezdy"
• The McMath-Pierce Solar Observatory
• Астронет > The McMath-Pierce Solar Observatory

DCSE . DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor. ... It offers lots of features such as color display of characters and structure, automatic alignment relative to sequences already aligned with others, sequence grouping, sequence or pattern searching, marker system and checking of incorporated RNA structure. tkDCSE is a version of DCSE for X-Windows. ... Home Site: . ... None . ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ...

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• The structure of files
• SAL- Numerical Analysis - Discrete Methods Related Tools - Rheolef
• SAL- Other Scientific Fields - Chemistry, Biology Related - RnaViz

A.V. Churakov, L.G. Kuz'mina, D.A. Lemenovskii . J.Organomet.Chem., v. 485, p. C81-C83 (1995) . ABSTRACT . The possibilities of functionalization Cp-ligands in p-complexes Ti, Zr and Hf are examined. Laboratory of Coordination Organometallic Compounds

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• Colloid-chemical phenomena in wastewater containing lignosulphonates
• Synthesis and Crystal Structure of Nitratocuprates(II) of Alkaline Metals and
• New titanium and zirconium sandwich and half-sandwich complexes containing the

. The UNIX file system is organised as a hierarchy of directories starting from a single directory called root which is represented by a / (slash). Imagine it as being similar to the root system of a plant or as an inverted tree structure. Immediately below the root directory are several system directories that contain information required by the operating system. The file holding the UNIX kernel is also here. UNIX system directories . Home directory . Pathnames .

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• Directories
• The Structure of HTML 3.0 Documents
• About the Concepts menu