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141. SDPsite - PF05175
... This family contains a protein with resolved 3D structure: Y882_METJA/25-193 , pdb ID: 1dus . SDPsite predicts following important positions (numbering corresponds to 1dus ): . ... 66Y, 165G, 163K, 139L, 190R, 85I, 140H, 136K, 173M . ... 138P, 137P, 69G, 71G, 136N, 175G, 65D, 35F . ... 136K, 137P, 138P, 139L, 140H . ... 163K, 165G, 190R . Mapping predictions onto structure of 1dus : . Associated grouping: . Group 1 . ...
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Ссылки http://bioinf.fbb.msu.ru/SDPsite/examples/PF05175.html -- 4.9 Кб -- 06.06.2008
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142. SDPsite - Algorithm Format requirements
... 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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Ссылки http://bioinf.fbb.msu.ru/SDPsite/algo.html -- 11.1 Кб -- 27.05.2008
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143. Untitled Document
((tr|Q9HWZ3:27.13469,(((((tr|Q97JG6:73.32871,sp|P52281:58.21097):22.08826, . (tr|Q8Y6Z1:50.97049,(tr|Q9KDW9:31.89890,(tr|Q99UH4:56.31642, . sp|P18156:43.43318):19.58605):11.29379):3.59077):71.07033, . (sp|Q51389:17.43830,((tr|Q8ZJK5:16.37272,sp|P11244:16.30590):17.93318, . sp|P44826:37.32225):18.11240):90.64721):85.73800, . tr|Q97P66:72.12900):67.97217,tr|P73809:39.02698):25.46760):7.46192, . ((tr|Q92ZW9:33.27410,tr|Q8UJW4:14.11857):8.47005, . sp|Q9L772:29.68911):15.56444,sp|P48838:30.29193); .
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Ссылки http://bioinf.fbb.msu.ru/SDPsite/tree.html -- 1.9 Кб -- 27.05.2008
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144. Alignment example
... MLNKLSAEFFGTFWLVFGGCGSAILAA--AFP------ELGIGFLGVALAF . ... SSLAPAG-FAPIAIGFGLTLIHLVSIPVTNTWVNPARSTG--VA--LF-----ADTAAL . ... MGRKLLAEFFGTFWLVFGGCGSAVFAA--AFP------ELGIGFTGVALAF . ... HGRVPAG-FAPIAIGLALTLIHLISIPVTNTSVNPARSTG--QA--LF-----VGGWAL . ... MSQT---STLKGQCIAEFLGTGLLIFFGVGCVA--ALKVAG------ASFGQWEISVI-W . ... ANQFTEG-LNPLIVGFLIVAIGISLGGTTGYAINPARDLGPRIAHAFL---PIPGKGSS . ... YPHFKATED-----QG-----AKLAVFSTDP-AIKHLPANFFSEVLGTFVLVLGILAIG- . ... MIDTSLATQFLGEVIGTAILIILGAGVVAGVSLKRSK------AENGGWVVITLAW...
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Ссылки http://bioinf.fbb.msu.ru/SDPsite/aln.html -- 7.6 Кб -- 27.05.2008
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145. Site Cluster
. The algorithm builds multiple alignment of conservative blocks and find consistent sets of helices. The input data may contain junk sequences. Department of Department of Bioengineering and Bioinformatics, MSU, Moscow, Russia . Mail to Andrey Mironov .
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Ссылки http://bioinf.fbb.msu.ru/RNAAlign/ -- 2.2 Кб -- 12.10.2006
[ Сохраненная копия ] Ссылки http://bioinf.fbb.msu.ru/RNAAlign/index.html -- 2.2 Кб -- 12.10.2006
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[ Сохраненная копия ] Ссылки http://bioinf.fbb.msu.ru/RNAAlign/index.html -- 2.2 Кб -- 12.10.2006
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146. Site Cluster
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Ссылки http://bioinf.fbb.msu.ru/RNAAlign/Buttons.html -- 1.7 Кб -- 12.10.2006
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147. Input Formats
... Recommended values . Start word length . Start length of motiff for Multiple sequence alignment. ... Max N Mismatches . ... Min score . ... Gap parameter . This parameter defines gap scoring. the grater this value is the stronger gap will be panalysed . ... If inforation content of a column is less than given value the column should be not included into alignment. the grater this value is the stronger gap will be panalysed . ... Max loop . Max energy of a helix . ... cgcatagctc cacca . ...
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Ссылки http://bioinf.fbb.msu.ru/RNAAlign/formats.html -- 7.8 Кб -- 12.10.2006
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148. RNA Alignment
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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Ссылки http://bioinf.fbb.msu.ru/RNAAlign/theory.html -- 2.8 Кб -- 12.10.2006
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149. SDPpred
... SDPpred is a tool for prediction of residues in protein sequences that determine functional differences between proteins, having same general biochemical function. ... Amino acid residues that determine differences in protein functional specificity and account for correct recognition of interaction partners, are usually thought to correspond to those positions of a protein multiple alignment, where the distribution of amino acids is closely associated with grouping of proteins by specificity. ...
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Ссылки http://bioinf.fbb.msu.ru/SDPpred/algo.html -- 18.4 Кб -- 25.03.2006
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150. SDPpred
GDE alignment format is one of standard alignment formats. A popular program for sequence alignment, Clustal, for example, can save alignment in this format. In this format, all letters indicating amino acids are in lower case, gaps are indicated by dashes. Sequences are placed one after another, name of each sequence is placed onto a separate line and begins with ?%?. The sequence is placed afterwards beginning on the next line and may be broken into several lines. ...
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Ссылки http://bioinf.fbb.msu.ru/SDPpred/gde.html -- 4.4 Кб -- 15.03.2006
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