... 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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• About authors ot this complex
• About this project
• Example of supporting positions

Geometrical core (core) is a maximal set of alignment positions such that C atoms in these positions are disposed similarly in ALL input protein chains. ... Minimal core size (#aa's) . ... Alternative core new atoms (%) . ... Geometrical core is a maximal set of alignment positions such that C atoms in these positions are disposed similarly in ALL input protein chain. ... Each input sequences is aligned to the corresponding sequence obtained from the ATOM section of the protein chain in the PDB file. ...

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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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• SDPlight
• SDPpred

... allpy/config.py: change min_width=4 previous value (min_width=3) was considered to be too low, that caused a lot of False Positives . ... 2 from allpy import dna . ... 6 def my_column_mark ( column , threshold ): . ... 8 count = {} . ... 11 count [ code ] = count . ... 12 for code in count : . ... 14 return "+" . ... 25 def find_runs ( markup ): . ... 33 plus_positions = [] . ... 46 raise Exception ( "No blocks in alignment" ) . ... 66 for column in alignment . ... 68 markup = alignment . ...

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• allpy: 2ede0318ff95 test/usecase2.py
• allpy: 6a50c2042d0e test/usecase2.py
• allpy: a3df15a42f9d test/usecase2.py

... 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 method for homologous recombination detection within bacterial species Anastasia S. Kalinina1, Alexandra L. Suvorikova Vladimir G. Spokoiny 1 1,2,4 , 1,3,4 , Mikhail S. Gelfand 1,5 A.A. Kharkevich ... of sexual reproduction in bacteria, transfer of DNA fragments from cell to cell and introducing these fragments into a genome by homologous recombination plays a major role in spreading beneficial mutations through the population ...

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• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/136.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/164.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/4.pdf

... 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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• Screening by similarity
• Screening of pattern or alignment against PROTEIN databank
• Genebee Predicted Annotation - Advanced

... MAST - Motif Alignment and Search Tool . ... 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. ... 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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Evalign . Evalign is a computerised evaluation method for protein sequence alignment algorithm. It compares computer alignments with structural alignments of protein sequences and tells how correct your sequence alignment program is. It gives additional information on the characteristics of different alignment algorithms and shows types specific failings in alignment. ... None . ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ... SAL@KachinaTech.COM . ...

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• SAL- Other Scientific Fields - Chemistry, Biology Related - SC_rate
• SAL- Other Scientific Fields - Chemistry, Biology Related - ClustalW
• SAL- Other Scientific Fields - Chemistry, Biology Related - GRS

Mustela . On a taxonomic position of the weasel (Carnivora, Mustela ) from the Cheju Island (South Korea) . ... The weasel from Cheju Island (formerly в?' Quelpart Island), which is situated in Korean Strait south of the coast of South Korea, was described as a separate species Lutreola quelpartis Thomas, 1908. ... Abramov A.V. 2000b. The taxonomic status of the Japanese weasel, Mustela itatsi (Carnivora, Mustelidae) // Zoologicheskii Zhurnal. ... A Pictorial Guide to the Mammals of Japan. ...

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• Taxonomic position of Eptesicus bobrinskoi - abstract
• Russian Journal of Theriology

... Форумы > Аспирантура > Тема . Автор темы ter . Форумы Список тем Новая тема . ... PhD positions in logic and AI, Vancouver (Canada) . PhD positions are available in the area of logic-based artificial intelligence. ... interested in logic (or discrete mathematics) and its uses for practical problem solving. ... Online application information is available at: . ... Следующая тема Предыдущая тема . ... Сайт работает с 29.08.2000, Copyright 2000 2011 MMOnline.Ru and MMForce.Net, . ...

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• MMOnline | Форумы | Аспирантура | PhD position in the University of Florida
• MMOnline | Форумы | Аспирантура | Phd positions at the Max-Planck Institute for
• MMOnline | Форумы | Аспирантура | PhD position at the University of Geneva,

... Кафедра общей экологии Биологического факультета МГУ им. М.В. Ломоносова и . ... Активные темы Список участников Поиск по форуму Помощь . ... Экологический Форум - Фундаментальная Экология : Предложения и замечания по сайту . Тема: to become in a position to those individu . ... Переход на форум -- Выберите форум -- О сайте "Фундаментальная экология" - Предложения и замечания по сайту Научные семинары - Научные семинары . Вы не можете публиковать новые темы в этом форуме . .