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
• Molecular biology databases
• About COGs

... 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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Computer tool for gene expression data processing and correlation analysis Anastasia M. Spitsina, Novosibirsk State University, 630090, Novosibirks, 2 Pirogova Str. , anastasia.spitsina@gmail.com Natalya ... databases (BioGPS (http://biogps.org/), GEO NCBI (http://www.ncbi.nlm.nih.gov/geo/)) has accumulated a large body of experimental data obtained using DNA microarrays ... So the aim of this work was to develop and improve own program for data processing and analysis of gene expression. ...

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• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/194.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/39.pdf
• http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/120.pdf

Database: . ... Affymetrix official site . ... Clone/Gene ID converter . ... Probe set search: . Affymetrix probe set identifier example: "238900_at" . ... Search . Text search: . Gene official symbol (*-wildcard) example: "c1orf*" . Word or phrase in gene official name example: "receptor" . ... Gene search: . ENSEMBL gene identifier example: "ENSG00000026508" . NCBI Entrez Gene identifier example: 7503 . HUGO gene identifier example: 1681 . ...

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

... 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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• BLAST Basic Overview

... annotate . ... Added fileio.File.read_alignment and fileio.File.write_alignment [closes #57] This is now the recommended interface. ... dendik@534 . ... 2 ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb/data/monomers/components.cif.gz . ... 3 codes_py = allpy/data/codes.py . ... 4 components_cif = allpy/data/components.cif . ... 6 all: doc codes tests . dendik@540 . ... 12 sphinx-autopackage --suffix = rst --dest-dir = docs/source/allpy/ allpy . ... 20 codes: $( codes_py ) . ... 23 rm $( codes_py ) . ...

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• allpy: NEWS annotate
• allpy: a17d913cccef NEWS
• allpy: 80043822a41e Makefile

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 -- Scientific Applications on Linux -- New Items Added in 1998/09 and
• SAL -- Scientific Applications on Linux -- New Items Added in 2000/11 and
• Sternberg Astronomical Institute

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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• Riordan R.M. - Seeing Data: Designing User Interfaces for Database Systems
• Raychaudhury S. - Computational text analysis for functional genomics and
• Attwood T.K., Parry-Smith D.J. - Introduction to bioinformatics :: Электронная

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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... The RPS-BLAST database must be prepared again for the small-endian system. ... Primary preprocessing Prepare the following files : i. a collection of PSI- BLAST -generated profiles with arbitrary names and suffix .chk; ii. a collection of profile master sequences , associated with the profiles , each in a separate file with arbitrary name and a 3 character suffix starting with c; the sequences can have deflines; they need not be sequences in nr or in any other sequence ...

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• http://kodomo.cmm.msu.su/FBB/year_04/doc/BLAST_help/impala.html
• http://kodomo.cmm.msu.ru/~molotok/Term3/blastp1
• http://kodomo.cmm.msu.ru/~ellys/links.html

Home . ... Activities . ... Laboratory of Mathematical Methods of Image Processing . Chair of Mathematical Physics . ... Image enhancement . ... Rank image filtering . Image analysis . ... Ringing effect . ... Database . ... Medical imaging . ... Multiresolution analysis and processing . ... The final version of the developed ringing database is available here: . ... The ringing extension of TID 2013 database: . ...