... day commit -- a lot of changes fasta.py: universal save_fasta() determine_long_line -- for determine length of fasta sequence string in user input everywhere: standart long_line=60 -- 70 blocK.sequences_chains: returns sequences in order as in project added monomer pdb_secstr to store secondary structure pdb adding: some improvements and fixes fix in from_pdb_ chain : use all peptides, not only first Sequence .pdb_files added to store information about pdb file for each ... monomers = monomers...

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• allpy: fb3164f03984 lib/sequence.py
• allpy: 6dfc736f37a9 lib/sequence.py
• allpy: b2ec17578145 lib/sequence.py

... 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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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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• Inquiry information || Distances
• Inquiry information || Rule of four sequences
• ETS sequence conservation

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
• S : rm_systems

TreeDL: a language for description of graph structures and operations on them" . Demakov A.V. Some methods of graph representation and processing in object-oriented languages are considered. Desirable features and a tool support of a language for description of graph structures and operations on them are analyzed. The TreeDL language having these features is described and compared with other approaches. PostScript (in Russian) (244KB) . ... Demakov A.V. e-mail: demakov@ispras.ru ...

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• "Implementation of the Lagrangian approach to the description of gas-particle

... 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 ::
• Peters C.A., Steenbrink J.H. - Mixed Hodge Structures :: Электронная библиотека

HMMER . The HMMER hidden Markov model software package and other software for large-scale genome analysis using probabilistic models of proteins and RNAs, from Sean Eddy's lab at Washington University, St. Louis USA. HMMER -- Hidden Markov models for sequence profile analysis. ... COVE -- an implementation of stochastic context free grammar methods for RNA sequence/structure analysis. ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ... SAL@KachinaTech.COM . ...

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• SAL- Other Scientific Fields - Chemistry, Biology Related - DCSE
• SAL- Other Scientific Fields - Chemistry, Biology Related - RnaViz

RNA Tertiary Structure Modelling . ... Two steps to fold coarse-grained model of RNA tertiary structure . ... fill in RNA secondary structure form with CT format (also with pseudoknots); . ... push "Finish Step #1" button to obtain secondary and intermediate* structures. * intermediate structure is the structure with minimum of "free energy" contains formed helixes and stacking, but without tertiary interactions . RNA secondary structure form . ... some useful RNA secondary structure databases: . ...

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• %TOPICTITLE% (9 vs. 10) - TWiki

... Research programm of the laboratory-chair< . ... Laboratory-chair of Discrete mechanics on a microscopic scale . ... Thus the structures of the physical world are not physical objects but physical processes. ... The primitive entity is called a material point. ... The value of the property “existence” of the material point varies from “the material point does not exist” to “the material point exists” by this process. ... Let call this structure a dynamical graph or a d-graph. ...

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. PHP Manual . Prev . Next . (3.0.13 - 3.0.18 only, PHP 4 >= 4.0.0) mcal_event_set_description -- Sets the description of the streams global event structure . int mcal_event_set_description ( int stream, string description) . mcal_event_set_description() sets the streams global event structure's description to the given string. Returns TRUE . Prev . Home . Next . mcal_event_set_title . Up . mcal_event_set_start

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• mailparse_msg_get_structure
• imap_fetchstructure
• xml_parse_into_struct

... 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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• Align tool for DNA-protein complexes
• Nhunt: program for nucleic acid sequence similarity search

Brain Research Group >> Research >> Change-point analysis ... << previous next >> . ... When detection of the change-points in alpha band power was performed as in the previous subsection, more than one change-point per second was obtained in average. ... The hypothesis of the hierarchy of EEG segmental descriptions (Kaplan 1998) (see subsection 7.3.2) is a theoretical reason for introducing the adjustment of the change-point detection probability. ...

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• Nonparametric approaches to the description of EEG piecewise stationary

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/2015/proceedings/abstracts/4.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/23.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/237.pdf

... DevHlp_Security This devhlp allows to open a file for read access in the Init routine of a BASEDEV . ... returned: size of file SYIOpenFile ends Valid at INIT time only. ... This routine uses the corresponding function of the miniFSD , not normal file I/O, thus access is restricted. ... Although the size argument of the data structure implies, I'd recommend to better not read more than 32K at a time. ... DL = 044h This function will return the table of security helper functions for file access. ...

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• Heliophysics, Internal structure and seismology
• Long description of example illustrating table row height calculations and

... A regular expression (regex) is a powerful way of specifying a complex search. MySQL uses regular Henry Spencer's inplementation of regular expressions. ... MySQL uses the extended version. This is a simplistic reference that skips the details. To get more exact information, see Henry Spencer's regex(7) manual page that is included in the source distribution. ... A regular expression describes a set of strings. The simplest regexp is one that has no special characters in it. ...

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• Kernel semid_ds structure
• Kernel msqid_ds structure
• Kernel shmid_ds structure

... Description . Catalog . ... In the Catalog, we publish equatorial (ЮБ 2000 , ЮД 2000 ) and galactic (l,b) coordinates of cluster centers derived as the position of overdensity in 2MASS catalog (Koposov et al. ... Distances, color-excesses and ages are the mean-square values calculated using all available evaluations from different color-magnitude diagrams. ... There are individual pages for every cluster where all available plots and parameters are published. ... 2002). ...

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• SAI OCL Catalog Structure
• SAI Open Star Clusters (SAI OCL) Catalog
• SAI OCL Catalog Virtual Observatory

... Таксон гамма-протеобактерии |Название таксона |GAMMAPROTEOBACTERIA | ... Поиск белка по |[swissprot-AccNumber:p00805*] |1 | ... выполняют функцию, сходную с функцией . ... гамма-протеобактерии|((([uniprot-Description:L-asparagi| | ... 1 |ASPG2_ECOLI |P00805 |ESCHERICHIA COLI |BACTERIA PROTEOBACTERIA | ... ENTEROBACTERIALES | ENTEROBACTERIACEAE ESCHERICHIA| ... 3 |Q31WL9_SHIBS |Q31WL9 |SHIGELLA BOYDII |BACTERIA PROTEOBACTERIA | ... 4 |Q32C26_SHIDS |Q32C26 |SHIGELLA |BACTERIA PROTEOBACTERIA | ...

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• Term 1
• Работа с системой SRS
• Pouliakhina's page

... Микс 193 A 131 A 171 A 211 A 304 A Корона Магнитограмма . 211 + 193 + 171 . Description . ... LASCO (Large Angle and Spectrometric Coronagraph)- инструмент на космическом аппарате SOHO, поставляющий изображения солнечной короны, на которых свет, идущий непосредственно от Солнца, заблокирован с помощью искусственного затмения, создаваемого самим аппаратом. ... The form and the location of the magnetospheric boundary are defined by pressure balance of the solar wind and geomagnetic field. ...

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... 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
• RNA Kinetics main page
• SDPsite

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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