Node ID 38888b46c342b9f51d12d4cd92947da07c7ad2c9 # Parent 2a6c2cffa891feca550fd7f18a9ad461600150c2 Added usecases from wiki to test / directory diff -r 2a6c2cffa891 -r 38888b46c342 test /usecase1.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ test /usecase1.py Fri Dec 17 00:45:20 2010 +0300 @@ -0,0 +1,35 @@ +from allpy import protein + +# Create sequences from string representation ...

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• allpy: df571a5233fb test/usecase2.py
• allpy: 38888b46c342
• allpy: 2b324332f6f7 allpy/block.py

... Alternative core new atoms (%) . ... An alignment of a set of structures is a set of positions , to each position some atoms from different structures correspond. ... Geometrical core of a set of structures is a subset of alignment positions those atoms are disposed similarly in all structures. ... For any two positions included into geometrical core, the distances between CA atoms of those positions in all structures may differ not more than the value of the parameter "Distance spreading". ...

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Alignment COG1325 . ... It is supported by 29 positions - that's written on the scheme. ... Such are positions number 5 ( leucine opposite isoleucine , valine and methyonine ), 30 ( glutamic acid opposite arginine , glycine and serine ), 51 ( threonine opposite alanine , phenylalanine and serine ), 55 ( phenylalanine opposite leucine , histidine and tyrosine ), 111 ( phenylalanine opposite isoleucine , leucine and valine ), 123 ( valine opposite isoleucine , ...

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• SDP home page
• About this project
• About authors ot this complex

... Minimal size of Clud clusters (residues) . ... An alignment of a set of structures is a set of positions , to each position some atoms from different structures correspond. ... Hydrophobic cluster of a single protein structure is a separated pool of nonpolar atoms. Usually there is the biggest cluster in the protein called hydrophobic core. ... ConClus program is able to detect of conservative hydrophobic clusters for a family of related protein domains or just for a set of aligned proteins. ...

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... 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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• SDPlight
• SDPpred
• SDPsite

... 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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Evalign . Evalign is a computerised evaluation method for protein sequence alignment algorithm. It compares computer alignments with structural alignments of protein sequences and tells how correct your sequence alignment program is. It gives additional information on the characteristics of different alignment algorithms and shows types specific failings in alignment. ... None . ... SAL Home | Other Scientific Fields | Chemistry, Biology Related . ... SAL@KachinaTech.COM . ...

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• SAL- Other Scientific Fields - Chemistry, Biology Related - SC_rate
• SAL- Other Scientific Fields - Chemistry, Biology Related - ClustalW
• SAL- Other Scientific Fields - Chemistry, Biology Related - GRS

... Advanced Screening by Similarity . ... Simple Query Form . Protein databanks: . ... Motif's length . threshold . Motif's power threshold . Alignment's power . ... of query sequence . End position of query sequence . ... Threshold of motif's . ... Threshold of alignment's . ... DNA/RNA Blosum 30 Blosum 50 Blosum 62 Dayhoff Johnson . ... Yes No . ... Sequence Alignment . ... Query sequence name . Enter or Paste here your Sequence without name OR Alignment . ...

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• RNA secondary structure prediction
• Screening of pattern or alignment against PROTEIN databank
• Genebee Predicted Annotation - Advanced

Mustela . On a taxonomic position of the weasel (Carnivora, Mustela ) from the Cheju Island (South Korea) . ... The weasel from Cheju Island (formerly в?' Quelpart Island), which is situated in Korean Strait south of the coast of South Korea, was described as a separate species Lutreola quelpartis Thomas, 1908. ... Abramov A.V. 2000b. The taxonomic status of the Japanese weasel, Mustela itatsi (Carnivora, Mustelidae) // Zoologicheskii Zhurnal. ... A Pictorial Guide to the Mammals of Japan. ...

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• Taxonomic position of Eptesicus bobrinskoi - abstract

Positioning of Nucleosomes at DNA Containing Short Periodic Sequences A.P Lifanov1,3, V.J. Makeev1,2, N.G. Esipova 1 2 1 V.A. Engelhardt Institute of Molecular Biology, Moscow, Russia Vavilov Institute of General Genetics, Moscow, Russia 3 johnnie_me@list.ru Nucleosome distribution, alongside with histone modifications and RNA polymerase II (Pol II) occupancy shows preferential association with exons ( ... Histogram of relative positions of nucleosome and exon borders is shown in Fig. ...

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• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/33.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/136.pdf
• http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/197.pdf

... Hale Bopp: A Continuing Tail . ... Credit Copyright: Guido Pizarro, ESO Explanation: Where is Hale-Bopp now? ... Clearly the comet still has a substantial tail , blown by the solar wind , that points generally away from the sunward direction. ... After a swing through the outer solar system and the Oort cloud , Hale-Bopp will pass through the inner solar system again ... around the year 5400. ... Publications with keywords: tail - Comet Hale-Bopp . Publications with words: tail - Comet Hale-Bopp . ...

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• Астронет > Hale Bopp: A Continuing Tail
• Waterton Lake Eclipse
• Journal "Peremennye Zvezdy"

... It interpolates the grid at the positions in the table and writes out the table with the interpolated values added as a new column. A bicubic [Default] or bilinear [ -Q ] interpolation is used, requiring boundary conditions at the limits of the region (see -L flag option). xyfile This is an ASCII [or binary, see -b ] file where the first 2 columns hold the (x,y) positions where the user wants to sample the 2-D data set. ... Default is 2 input columns]. -bo Selects binary output. ...