... 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: 2ede0318ff95 test/usecase1.py
• allpy: ee2c10aa74b8
• allpy: 2ede0318ff95 allpy/protein.py

... 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

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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• SVETKA, a program for multiple sequence alignments analysis
• PLANdbAffy: probe-level annotation database for Affymetrix expression

... 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

Application of evolutionary model in the evaluation of the quality of pair wise alignment of amino acid sequences Valery Polyanovsky, V. G. Tumanyan Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia ... : polyanovskyvo@mailfrom.ru, tuman@eimb.ru The purpose of the work is to develop a universal method for estimating the pairwise alignment quality depending on the evolutionary distance (degree of homology) between the ... REFERENCES 1. ...

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• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/156.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/161.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/164.pdf

... Instructions are in README.TXT file inside the tarball. ... tar -xvf nhunt_x86.tar Query and database files should contain sequences in FASTA format ( wikipedia description ). ... Default name of the output file is 'nhunt.out'. ... Any parameter consists of key and value and is called as '-key value', where 'key' is one character and 'value' is any number of characters. -i Query file . ... No default value. -d Database file . ... No default value. -o Output file . ... Default value: 'nhunt.out' . ...

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• ConClus
• Nhunt

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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• Changeset 120:a8549a69f959 тАУ Python Battle
• Множественное выравнивание.
• Changeset 63:27a43636ab6e тАУ Python Battle

... Submitted Sequences: . ... Results 1.REFINED ALIGNMENT Power 4.27 Homology percent 5.3 Symbols used in the alighnment charts: ' ' - average weight of column pair exchanges is less than weight matrix mean value '.' - is less than mean value plus one SD '+' - is less than mean value plus two SD '*' - is greater than mean value plus two SD .. ... SQ1 ( 48) yhtcggillnSHWVLTAAHCFKNKkkvt SQ2 ( 46) srqtfsirsiSQNGYDPRQNLNDVL--- SQ3 ( 1) ----------SRRTYTLTDYLKSTFr-- 5TH LOCAL SUPERMOTIF, power 2.51 + *.. ...

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• RNA secondary structure prediction
• AliGraf - GeneBee Graphical Alignment Help
• AliComp - GeneBee Alignment Comparison Help

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) ::

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 - ClustalW
• SAL- Other Scientific Fields - Chemistry, Biology Related - DCSE
• SAL- Other Scientific Fields - Chemistry, Biology Related - HMMER

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

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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. ...