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281. ОБЗОРЫ
... Проблема реконструкции конкретного хода эволюционного процесса и построения филогенетических деревьев остается неизменно актуальной задачей, поскольку эволюционная трактовка результатов исследования является имманентной частью биологического мышления. ... Суть предлагаемого нами принципа максимального топологического подобия состоит в реконструкции дерева, имеющего структуру, в максимальной степени отражающую сведения о взаимном отношении объектов, содержащиеся в исходных данных. ...
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Ссылки http://www.genebee.msu.ru/services/papers/CHUMAKOV/chumakov.htm -- 34.8 Кб -- 15.10.2001
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282. GeneBee DotHelix Motifs' Map Help
... When the standard constant M=M(W) is chosen, a large number of the obtained motifs will be "noise", despite their formal statistical significance. This fact, obstacling further alignment construction by increase of the search, is caused by the null hypothesis of independence of the sequence being aligned (indeed, the very desire to align sequences is an evidence of their dependence!) ... If 80% or more of the characters in a sequence are as above, then DNA / RNA is assumed, protein otherwise. ...
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Ссылки http://www.genebee.msu.ru/services/dhm/help.html -- 19.4 Кб -- 15.10.2001
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283. http://www.genebee.msu.ru/services/papers/BIOSYS_30/BIOSYST.DOC
Construction of the full local similarity map for two biopolymers A. M. Leontovicha , L. I. Brodskyb and A. E. Gorbalenyac "A. N. Belozersky Institute of Physical and Chemical Biology, Moscow State University, Moscow, 119899, Russia, bGandalf Ltd., ... The first one is the alignment of two monomer sequences. The second one is the construction of the so-called "local similarity map" (dot matrix) which maps pairs of similar fragments of coinciding lengths (without insertions and deletions). ...
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Ссылки http://www.genebee.msu.ru/services/papers/BIOSYS_30/BIOSYST.DOC -- 154.5 Кб -- 15.10.2001
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284. BioSystems, 30 (1993) 57-63 57
BioSystems, 30 (1993) 57-63 Elsevier Scientific Publishers Ireland, Ltd. Construction of the full local similarity map for two biopolymers . ... A novel algorithm for construction of complete maps of local similarity for two biopolymer sequences is described. ... Two approaches to this problem exist. ... The second one is the construction of the so-called "local similarity map" (dot matrix) which maps pairs of similar fragments of coinciding lengths (without insertions and deletions). ...
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Ссылки http://www.genebee.msu.ru/services/papers/BIOSYS_30/BIOSYST.htm -- 32.7 Кб -- 12.10.2001
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285. Phylogenetic tree
... Chumakov K.M. and Yushmanov S.V. The maximum topological similarity principle in molecular systematics, Mol. ... Yushmanov S.V. and Chumakov K.M. Algorithms of the maximum topological similarity phylogenetic trees construction, Mol. ... Building of probable phylogenetic trees is bases on the matrix of pair distances between sequences. ... The algorithm is aimed at construction of the tree, for which this number is minimal, i.e the maximum topological similarity tree. ...
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Ссылки http://www.genebee.msu.ru/services/hlp/phtree-hlp.html -- 15.2 Кб -- 11.10.2001
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286. http://www.genebee.msu.ru/services/papers/CHUMAKOV/chumakov.doc
Прицип Максимального Топологического Подобия в Молекулярной Систематике К.М. Чумаков, С. В. Юшманов Межфакультетская проблемная НИЛ молекулярной биологии и биоорганической химии им. А.Н.Белозерского МГУ Проблема реконструкции конкретного хода эволюционного процесса и построения филогенетических деревьев остается неизменно актуальной задачей, поскольку эволюционная трактовка результатов исследования является имманентной частью биологического мышления. ... Длины всех ребер дерева не отрицательны. ...
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Ссылки http://www.genebee.msu.ru/services/papers/CHUMAKOV/chumakov.doc -- 91.0 Кб -- 11.10.2001
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287. RNA secondary structure prediction
... 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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Ссылки http://www.genebee.msu.ru/services/hlp/rna2-hlp.html -- 9.1 Кб -- 11.10.2001
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288. Screening of pattern or alignment against PROTEIN databank
... HELP ON SCREENING OF PATTERN OR ALIGNMENT AGAINST PROTEIN PROTEIN . ... The method of looking for all pattern entries (possibly inexact) in PROTEIN databank is almost the same as in PROSITE screening procedure. ... The screening by query alignment, based on the same principle: the alignment is seen as a pattern defining letter's frequencies in every position. The pattern example: . ... the only one capital letter at a position means that only given residue should be at the position. ...
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Ссылки http://www.genebee.msu.ru/services/hlp/pat-hlp.html -- 5.6 Кб -- 11.10.2001
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289. Screening protein sequence against PROSITE databank
... HELP ON SCREENING PROTEIN SEQUENCE AGAINST PROSITE DATABANK . ... One of the methods to select the functionally important protein sequence fragment is to compare the sequence with PROSITE databank, that collects all patterns (rules of the sequence fragment construction) for biochemically important protein fragments along with it's description. ... The method of screening is described in Biochemistry (Moscow) (Brodsky L. et al., v.60, №8, pp. ... QUERY SEQUENCE: (should be in one-letter code format):...
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Ссылки http://www.genebee.msu.ru/services/hlp/prosite_hlp.html -- 5.1 Кб -- 11.10.2001
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290. http://www.genebee.msu.ru/services/papers/GNB-NET/GNB-NET.DOC
... Basic server procedures are dedicated to homology (similarity) search of sequence and 3D structure of proteins. The homologies found could be used to build multiple alignments, predict protein and RNA secondary structure, and construct phylogenetic trees. ... KEY WORDS: mathematical and statistical biology, biological sequences databanks, macromolecular algorithms, sequence homology, sequence alignment, RNA secondary structure, protein secondary and tertiary structure, protein structure alignment. ...
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Ссылки http://www.genebee.msu.ru/services/papers/GNB-NET/GNB-NET.DOC -- 1459.0 Кб -- 11.10.2001
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291. Biochemistry (Moscow), Vol
1995, Biochemistry, 60, 8, 923-928. ... Basic server procedures are dedicated to homology (similarity) search of sequence and 3D structure of proteins. The homologies found could be used to build multiple alignments, predict protein and RNA secondary structure, and construct phylogenetic trees. In addition to traditional methods of sequence similarity search, the authors propose "non-matrix" (correlational) search. ... RNA Secondary Structure Prediction Based on Sequence Alignment . ...
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Ссылки http://www.genebee.msu.ru/services/papers/GNB-NET/GNB-NET.htm -- 27.2 Кб -- 11.10.2001
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292. DIMACS Series in Discrete Mathematics
... Local similarities and pairwise sequence alignment . ... Multiple sequence alignment . ... This includes representation in corresponding databases of information about structurally and functionally important fragments and patterns, taking into account obtained statistical information about sequences and three-dimensional structure data. ... The alignment procedure for each shift of the sequences finds in the local similarity map a series of non-overlapping diagonal segments and computes its power. ...
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Ссылки http://www.genebee.msu.ru/services/papers/DIMA-BRO/DIMA-BRO.htm -- 47.5 Кб -- 11.10.2001
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293. DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume
DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume 8, 1992 . ON THE OPTIMALITY OF THE DAYHOFF MATRIX FOR COMPUTING THE SIMILARITY SCORE BETWEEN FRAGMENTS OF BIOLOGICAL SEQUENCES . ... In this case letter frequencies (that are parts of (6) and (7)) can be computed using either the entire sequences (see (1)) or the fragments under consideration. ... Consider in more detail the case when the letter frequencies are computed using the entire sequences (i.e. by formula (1)). ...
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Ссылки http://www.genebee.msu.ru/services/papers/DIMA-LEO/DIMA-LEO.HTM -- 57.1 Кб -- 08.10.2001
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294. V
The Building of Multiple Alignment Using the Method of Iterative Dynamic Improvement of the Initial ?Motif? Alignment . V.K. Nikolaev 1 , A.M. Leontovich 2 , V.A. Drachev 2 , L.I. Brodsky 1,3 . ... In the article there were studied the optimality and the quality of restoration of the true alignment?s columns depending on initial alignment with it?s iterative dynamic improvement [1]. ... On the abscissa axis for all 3 graphs the quality of true alignment column restoration in priming is measured. ...
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Ссылки http://www.genebee.msu.ru/services/papers/MA_NIK/MA_NIK.htm -- 47.4 Кб -- 07.10.2001
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295. http://www.genebee.msu.ru/services/papers/MA_NIK/MA_NIK.DOC
The Building of Multiple Alignment Using the Method of Iterative Dynamic Improvement of the Initial ?Motif? Alignment V.K. Nikolaev1, A.M. Leontovich2, V.A. Drachev2, L.I. Brodsky1,3 1Gendalf Ltd., ... In the article there were studied the optimality and the quality of restoration of the true alignment's columns depending on initial alignment with it's iterative dynamic improvement [1]. ... On the abscissa axis for all 3 graphs the quality of true alignment column restoration in priming is measured. ...
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Ссылки http://www.genebee.msu.ru/services/papers/MA_NIK/MA_NIK.DOC -- 369.5 Кб -- 02.10.2001
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296. http://www.genebee.msu.ru/services/papers/DIMA-LEO/DIMA-LEO.DOC
ON THE OPTIMALITY OF THE DAYHOFF MATRIX FOR COMPUTING THE SIMILARITY SCORE BETWEEN FRAGMENTS OF BIOLOGICAL SEQUENCES A.M. leontovich institute of physico-chemical problems in biology, laboratory bldg. ... The exact numerical value of this measure depends on the choice of the letter substitution weight matrix that characterizes the similarity of individual letters (nucleotides or amino acid residues) constituting the compared sequences. ... Hence A is a natural similarity measure for fragments. ...
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Ссылки http://www.genebee.msu.ru/services/papers/DIMA-LEO/DIMA-LEO.DOC -- 635.0 Кб -- 30.09.2001
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297. AliComp - GeneBee Alignments Comparison - Advanced
... GeneBee . ... ALiComp - GeneBee Alignments Comparison . ... 1st alignment . ... 2nd alignment . Comparison Picture Options . ... Offsets comparison Column values comparison Col. values comparison 2 . ... Picture Options for Separate Alignment Images . ... DNA/RNA Dayhoff Johnson Blosum 30 Blosum 50 Blosum 62 Pam 60 Pam 120 Pam 250 Gonnet 120 Gonnet 250 Gonnet 350 . ... None All groups Max group at column Column values Column values (best-to-worst) . ... First alignment ( Example ) . ...
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Ссылки http://www.genebee.msu.ru/services/alicomp/advanced.html -- 24.7 Кб -- 26.08.2001
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298. AliComp - GeneBee Alignment Comparison Help
AliComp - GeneBee Alignment Comparison Help Type in a title for this session for you to remember. ... First alignment: .* ... HCVPCP2 ( 279) LLSVTSVVM------VGGYVAPVNTVKPKPVINQ TGVPCP2 ( 277) AIASNFVVKK-PQAEERPKNCAFNKVAASPKIVQ MHVPCP2 ( 288) CLYLKNLKQTFSSVLTTFYLDDVKCVEYKPDLSQ MHVPCP1 ( 272) GYGMTFSMSPFELAQLYGSCITPNVCFVK----- HCVPCP1 ( 262) TICIKDADY---NAKVEISVTPIKN--------- TGVPCP1 ( 256) TLFINANVM--TRAEKPKQEFKVEKVEQQPIVEE IBVPCP ( 282) AMYTRFAFK----NETSLPVAKQSKGKSKS-VKE Second alignment : ...
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Ссылки http://www.genebee.msu.ru/services/alicomp/help.html -- 20.1 Кб -- 26.08.2001
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299. AliComp - GeneBee Alignments Comparison - Advanced
. Homepage . Belozersky Institute . GeneBee . Russian EMBnet Node . ALiComp - GeneBee Alignments Comparison . Help . Advanced query . Alignment title . Picture types . Offsets comparison Column values comparison Col. values comparison 2 . First alignment ( Example ) . Second alignment ( Example ) . Last updated: August 26 2001. Comments and bug-reports send to: nik@genebee.msu.su
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Ссылки http://www.genebee.msu.ru/services/alicomp/basic.html -- 17.2 Кб -- 26.08.2001
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300. TreeTop - Phylogenetic Tree Reconstruction
... TreeTop - Phylogenetic Tree Prediction . The source sequence multiple alignment could be formed from low and upper case letters. Upper case letters will show that there is a homology between correspondent fragments in alignment. ... Algorithm . Cluster + Topological Cluster Topological . ... DNA/RNA Blosum 62 Blosum 50 Blosum 30 Dayhoff Johnson . ... Picture Options . ... None Slanted Slanted 2 Rectangular Rectangular 2 Phylogram Unrooted Unrooted 2 . ... cluster algorithm . ...
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Ссылки http://www.genebee.msu.ru/services/phtree_full.html -- 9.8 Кб -- 16.06.2001
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