... Both sequences must be either nucleotides or proteins. ... For blastx 1st argument should be nucleotide [String] default = blastp -g Gapped [T/F] default = T -o alignment output file [ File Out] default = stdout -d theor. db size ( zero is real size) [ Integer ] default = 0 -a SeqAnnot output file [ File Out] Optional -G Cost to open a gap ( zero invokes default behavior ) [ Integer ] default = 0 -E Cost to extend a gap ( zero invokes ...

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• http://kodomo.cmm.msu.su/FBB/year_04/doc/BLAST_help/blastall.html
• http://kodomo.cmm.msu.su/FBB/year_04/doc/BLAST_help/rpsblast.html
• http://kodomo.cmm.msu.su/FBB/year_04/doc/BLAST_help/blastclust.html

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins . The Pfam plain text format is one of the formats, in which aligned sequences from the Pfam database can be retrieved. For the correct work of SDPpred gaps are required to be indicated by dashes and all letters indicating amino acids are required to be in upper case. ... TIPA_PHAVU/13-234 EATHPDS--MRASLAEFASTFIFVFAGEG--SGLALVKIYQ- . ... back to input format rules . ...

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• Molecular biology databases
• SVETKA, a program for multiple sequence alignments analysus
• About COGs

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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... 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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• Nhunt

... Protein sequences: . ... OWL : non-redundant database assembled from a number of primary sources including translations of nucleic acid sequences (Swissprot, PIR, NRL3-D and GenPept). ... Database of protein families and HMMs (collection of multiple sequence alignments and hidden Markov models) . ... Collection of protein families constructed by clustering all complete protein sequences in SwissProt. ... The Genome Sequence Database: complete relational database of DNA sequences and annotation . ...

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• GeneBee BLAST 2.2.22+ Services Help
• GeneBee BLAST 2.2.8 Services Help
• BLAST Basic Overview

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/2013/abstracts/abstracts/39.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/215.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/222.pdf

You can search database for submitted information. ... Character * specifies arbitrary character sequence (eg. '*n' will result: John, Martin etc.) Character * is placed at end of line automatically ('Mar*' = 'Mar' will result: Martin, Martina etc.) Blank form will result ALL database records. ... Family name: . ... Topic: . ... Seismo-tectonics of Tsunami 3. Numerical and Analytical Models of Local Tsunami Behavior 4. ... Recent Local Tsunamis 8. ... Information . ... Database search . ...

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PHP Manual . ... Persistent connections are SQL links that do not close when the execution of your script ends. ... People who aren't thoroughly familiar with the way web servers work and distribute the load may mistake persistent connects for what they're not. ... For example, if you had 20 different child processes that ran a script that made a persistent connection to your SQL server, you'd have 20 different connections to the SQL server, one from each child. ... Connection handling . ...

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• InterBase functions
• Database (dbm-style) abstraction layer functions
• fbsql_read_blob

Электронная библиотека Попечительского совета . ... Brown S.M. - Bioinformatics: A Biologist's Guide to Biocomputing and the Internet . ... Название: Bioinformatics: A Biologist's Guide to Biocomputing and the Internet . Автор: Brown S.M. Аннотация: . A practical overview of bioinformatics, for researchers. ... Also discusses and evaluated programs for PCs, the Internet, and mainframes. DLC: Bioinformatics. ... Электронная библиотека попечительского совета мехмата МГУ , 2004-2016 . ...

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• Gossett E. - Discrete Math with Proof :: Электронная библиотека попечительского
• Lander E.S., Waterman M.S. (eds.) - Calculating the Secrets of Life:
• Bishop M.J. - Genetic Databases (Biological Techniques Series) :: Электронная

... About lab . ... Online Journal "Computer graphics and multimedia" (in russian) . ... We found that automatic models are significantly worse at predicting attention than even single-observer eye tracking. We propose a semiautomatic approach that requires eye tracking of only one observer and is based on time consistency of the observer?s attention. ... Gitman Y, Erofeev M, Vatolin D, Bolshakov A, Fedorov A. Semiautomatic Visual-Attention Modeling and Its Application to Video Compression . ...

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• Semiautomatic Visual-Attention Modeling | Лаборатория компьютерной графики и
• Video Frame Rate N-Times Up-Conversion | Лаборатория компьютерной графики и
• Video Frame Rate N-Times Up-Conversion | Graphics and Media Lab

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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• WWW gateway to SAI databases
• SAL- Database Systems - Utilities Other DBMS - c-tree Plus
• Sternberg Astronomical Institute

... Length = 4702289 Score = 751 bits (1939), Expect = 0.0 Identities = 359/457 (78%), Positives = 409/457 (89%) Frame = -2 Query : 1 MSVQQIDWDLALIQKYNYSGPRYTSYPTALEFSEDFGEQAFLQAVARYPERPLSLYVHIP 60 MS I WDL+LIQKYNYSGPRYTSYPTALEFSED+ E AF QAV RYP+RPLSLYVHIP Sbjct : 3930889 MSEHAIVWDLSLIQKYNYSGPRYTSYPTALEFSEDYNESAFQQAVKRYPQRPLSLYVHIP 3930710 ...

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• allpy: a1307c0bb030 test/usecase1.py
• allpy: a17d913cccef test/usecase1.py
• allpy: a17d913cccef allpy/markups.py

XAFS spectroscopy is widely used in physics, materials science, chemistry (especially in catalysis and coordination chemistry), biology, geochemistry and environmental science. ... This is an interface to the Glimpse -based search engine which enables you to find published papers in different fields of x-ray absorption spectroscopy -- XAFS, EXAFS, XANES, NEXAFS, SEXAFS, XEOL, and EXAFS-like phenomena in photoemission, electron-energy-loss spectra and so on. ... Database Search Form . ...

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. ЭКОЛОГИЧЕСКАЯ ИНФОРМАЦИЯ . WEB- ориентированная библиографическая база данных .

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... Alexey D. Neverov . ... Department of Bioengineering and Bioinformatics, Moscow State University. State Scientific Center GosNIIGenetika. ... EDAS human . EDAS mouse . EDAS dog (not availible now) . EDAS rat (not availible now) . To navigate this site please install the latest version of Macromedia Flash Player for Windows or for Linux . If you do not wish to install Flash you could use text pages with less functionality. ...

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• Alternative Splicing DataBase.
• EDAS (human) - Alternative Splicing DataBase.
• EDAS (mouse) - Alternative Splicing DataBase.

Integration of Fuzzy c-Means Clustering algorithm with PostgreSQL database management system" . Miniakhmetov R.M., Tsymbler M.L. The integration of data mining algorithms with relational database management systems (DBMS) is a topical issue. ... This paper suggests an implementation of Fuzzy c-Means Clustering algorithm for the PostgreSQL open-source DBMS. ... Keywords: fuzzy clustering, integration clustering algorithms with relational DBMS . PostScript (in Russian) (787KB) . ...

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• "Identification algorithms for substances in the hybrid database on molecular
• Using Intel Xeon Phi coprocessors for execution of natural join on compressed
• "Effective buffer management replacement algorithm for parallel shared-nothing

About BAFIZ . ... BAFIZ is a program devoted to the development of a distributed network of the knowledge and data bases for research of fundamental properties of the matter and applied nuclear physics. The project sponsored by Russian Foundation of Basic Research , RFBR reference number is 95-07-19502. ... This Page is developed at Laboratory of Computational Mathematics, . ... Last updated on 2 September 1999 . Copyright 1999 Laboratory of Computational Mathematics (DRCM) ...

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... Apache HTTP Server Version 2.0 . ... htdbm is used to manipulate the DBM format files used to store usernames and password for basic authentication of HTTP users via mod_auth_dbm . ... mod_auth_dbm . ... Web password files such as those managed by htdbm should not be within the Web server's URI space -- that is, they should not be fetchable with a browser. ... The MD5 algorithm used by htdbm is specific to the Apache software; passwords encrypted using it will not be usable with other Web servers. ...

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• Initalize Database Mode
• Rebuild Database Mode
• DPRODUCT

Laboratories \ Laboratory of Avian's Ecology and Behaviour Control \ Goals and Tasks . Goals and Tasks . ... Ecology of organisms and communities . ... Bioacoustics and biolinguistics of birds . ... The number and distribution of rare bird species in Moscow Region were studied in the course of preparation of the new edition of the Red Data Book of Moscow Region. ... On the basis of the Laboratory a Research Group of Avian Ecology (RGAE) is working. ... In the Laboratory . ...

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• A.N. Severtsov Institute of Ecology and Evolution (IPEE RAS): Site News: Site
• Laboratories: Laboratory for behavior and behavior ecology of mammals:
• A.N. Severtsov Institute of Ecology and Evolution (IPEE RAS): News: News:

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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• SDPsite - Gallery of examples
• Input Formats
• SDPsite - Algorithm Format requirements