... annotate . ... lib.block -- copy of sequences --> link to old sequences, when create from block . ... BurkovBA@0 . ... 5 import project . ... bnagaev@129 . ... 15 * self.project -- project object, which the block belongs to . ... 18 * self.positions -- sorted list of positions of the project.alignment that . ... bnagaev@112 . 30 def __init__ ( self , project , sequences = None , positions = None ): . ... 39 positions = range ( len ( project )) . ... project = project . ... project , self . ...

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• allpy: NEWS annotate

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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• SVETKA, a program for multiple sequence alignments analysis
• Geometrical core

... Query: E. coli K12 tRNA (valV, selC, asnV, leuT, argZ from EMBL entry U00096 ) . ... BLASTN (both) | ... Nhunt . ... BLASTN (optimal): 3.5 s . BLASTN (default): 0.8 s . ... Nhunt: 7 s The program Nhunt surpass all other tested programs in sensitivity. ... Nhunt BLASTN (optimal): 2.9 s . ... Nhunt: 3.7 s BLASTN with default parameters actually cannot find any significant homologues. ... Nhunt-3: 1.7 s BLASTN with default parameters actually cann't find any significant homologues. ...

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• ConClus

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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• SVETKA, a program for multiple sequence alignments analysus
• SVETKA, a program for multiple sequence alignments analysis
• ETS sequence conservation

Home page . ... GeneBee . ... A4 - Genebee Adaptive Automated Annotation . ... Home . Advanced query . Annotation title . ... ITA[1,1] ITA[0,1] USUAL . Additional output . ... NRAS_1 MTEYKLVVVG AGGVGKSALT IQLIQNHFVD EYDPTIEDSY RKQVVIDGET CLLDILDTAG QEEYSAMRDQ VFAINNSKSF ADINLYREQI KRVKDSDDVP MVLVGNKCDL PTRTVDTKQA HELAKSYGIP GVEDAFYTLV REIRQYRMKK LNSSDDGTQG CMGLPCVVM . ... Last updated: December 23, 2008. ...

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• Genebee Predicted Annotation - Advanced
• Genebee Predicted Annotation Help
• AliGraf - GeneBee Graphical Alignment Help

... 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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• Task 9 (sequence annotation)
• Global and Local Alignment of A.A Sequences

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) ::

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/197.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/161.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/164.pdf

Given word length and max number of mismatches . Use MEME algorithm for define conserved blocks . Apply the Dynamic programming algorithm to create chain of the blocks . Refine the chain using combined profile for chain of blocks. ... Reduce word length and number of mismatches and repeat the procedure for spacer between the blocks. ... Create helix profile and apply MEME-like iterative procedure to find sets of helices that consistent lokated reative to conserved blocks . ...

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• Input Formats
• SDPpred
• SDPsite - Algorithm Format requirements

RnaViz . RnaViz is a user-friendly, portable, windows-type program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure can be changed easily. ... Home Site: . http://rrna.uia.ac.be/rnaviz/ . ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ... SAL@KachinaTech.COM . ...

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• SAL- Other Scientific Fields - Chemistry, Biology Related - Evalign
• SAL- Other Scientific Fields - Chemistry, Biology Related - PomBase
• SAL- Other Scientific Fields - Chemistry, Biology Related - DCSE

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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SCIENTIFIC TASKS AND RESULTS . In the results of searching for new perspective solid state materials for the quantum electronics, non-linear optics and other fields of physics more than 200 various oxide compounds were synthesized and peculiarities of their atomic structure and physical properties are studied. Single crystals of 80 such the compounds are grown and thoroughly investigated. ... A family of oxide-ion conductors on the base of La 2 Mo 2 O 9 (30.10.09) . ... Main page ...