... 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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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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• Inquiry information || Rule of four sequences

Expands the parameters to the query that was used to display the page. ... Parameters: . format="..." format string for each entry, default $name=$value . ... encoding="..." the encoding to apply to parameter values; see ENCODE for a description of the available encodings. ... Name of the parameter . ... String value of the parameter. Multi-valued parameters will have a "row" for each value. ... QUERYPARAMS{format="<input type='hidden' name='$name' value='$value' encoding="entity" />"}% . ...

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• %TOPICTITLE% (1 vs. 2) - TWiki
• VarQUERYPARAMS - TWiki - TWiki

Scoring Matrices . Matrix Sequences Sequence Consisting of the first four Amino Acids in the Protein GYRB_ECOL: . ... Sequence Achieved by Substitution of the 2nd and 4th Amino Acid and Insertion between the 3d and 4th Amino Acid, in the Protein GYRB_ECOLI, to randomly chosen new amino acids: . ... Matrix Sequences Sequence Consisting of the First Nine Amino Acids of the Protein GYRB_ECOLI: . ... Sequence Consisting of 2nd, 3d, 7th, 8th and 9th Amino Acid Residues of the Protein GYRB_ECOLI: . ...

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Next: Other parameters of the Up: The Model Previous: Initial binary parameters . As we only deal with initially massive binary systems (their primary's mass is higher than 10 ), which are capable of evolving off the main sequence during less than years, the compact stars left behind stellar evolution are (in the case of the most massive stars) NSs and BHs. ... For a NS belonging to a binary, the evolution complicates as the secondary star evolves: for example, (recycling), etc. ...

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• Parameters of binary compact star evolution
• The Effect of Relativistic Wind on Accretion Flow Parameters
• Evolutionary Scenarios of Binary Systems

... 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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... Next: Index Up: Scanning Probe Microscopy Image Previous: COM-port initialization file format Contents Index . Figure D.1: Parameters of 3D Images . ... Intensity of material emission (Mat. ... material color for diffused light (Mat. ... material reflection color for directed light (Mat. ... material reflection color for reflected light (Mat. ... intensity of directed light (Light Diffuse) . ... Material Shininess) In our case we use the model, where , and this parameter is called Material Color. ...

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• Scan parameters

... This gropup of options allows You to change the following speech recording parameters: . ... This gropup of options allows You to change the following parameters of linear prediction: coefficients calculation: . ... This gropup of options allows You to change the following speech processing parameters: . ... This gropup of options allows You to change the following speech recognition parameters: . ... This gropup of options allows You to change the following speech detection parameters: . ...

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• Options

... x264 is an open source codec of standard MPEG4 AVC/H.264, developed by programmers from all over the world. ... Accumulated during previous frames' compressions statistic is actively used by codec to improve effectiveness of adaptive models. ... These parameters are used only before encoding start, so, our improvements are more significant for short sequences. ... 3 Results of codec x264 modification on "flower" sequence . ... 5 Results of codec x264 modification on "flower" sequence, low bitrates ....

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• x264 codec improvement | Лаборатория компьютерной графики и мультимедиа
• Algorithms for calculating parameters of virtual scenes in computer vision

Next: Items that Define Paths Up: The sendmail.cf File Previous: An Example sendmail.m4 File . A few or the items in the sendmail.m4 file are required all the time; others can be ignored if you can get away with defaults. The following sections describe each of the items in the example sendmail.m4 file in more detail. Items that Define Paths . Defining the Local Mailer . ... Domain Name Service Related Items . Defining Names the Local System is Known by . UUCP-Related Items . ...

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• Ethernet Autoprobing

... 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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• OUTPUT
• Screening by similarity
• Screening of pattern or alignment against PROTEIN databank

... New parameter parsing API: This chapter documents the new Zend parameter parsing API introduced by Andrei Zmievski. ... It greatly simplifies the process of receiving parameteres, but it has a drawback in that it can't be used for functions that expect variable number of parameters. ... The third argument is a string that specifies the number and types of arguments your function is expecting, similar to how printf format string specifies the number and format of the output values it should operate...

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• odbc_procedurecolumns
• udm_set_agent_param
• udm_get_res_param

... Reducing trigonometric expressions . Heuristics for trigonometric expressions . ... If some parameters appear to be the elements of the orthogonal matrix such as quark mixing Cabbibo-Kobayashi-Maskava matrix, one should declare them by the statement OrthMatrix( {{ , , }, { , , }, { , , }} ). where denote the parameters. ... If the substitution for one angle combination is defined, LanHEP offers to define the other ones for expressions consisting of parameters used in previous SetAngle statements. ...

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• Structure of LanHEP input file
• General structure
• Fortran case

... The RADEN data bank produced at the Department of Chemistry of Moscow State University is designed as well to accumulate published information on radiative parameters of diatomic molecules, as to analyse it and recommend the more reliable values. ... electronic transition moments D ( R ); . ... dipole moments, . ... FACTUAL RECOMMENDED DATABASE contains now the ab initio and experimental electronic transition moments for more than 250 band systems which belong to more than 100 diatomic molecules. ...

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I have dropped the differentiation of HTML into a sequence of conformance levels. ... This (and upward compatible specifications) define the Internet Media Type (RFC 1590) and MIME Content Type (RFC 1521) called "text/html". The type "text/html" accepts the following parameters: . ... Character sets . The charset parameter (as defined in section 7.1.1 of RFC 1521) may be used with the text/html content type to specify the encoding used to represent the HTML document as a sequence of bytes. ...

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• Security Considerations

... Querying File Parameters . Up: File Manipulation Next: File Info Previous: Querying the Size of a File . MPI_FILE_GET_GROUP(fh, group) . ... OUT group] group which opened the file (handle) . int MPI_File_get_group(MPI_File fh, MPI_Group *group) . MPI_FILE_GET_GROUP(FH, GROUP, IERROR) . ... MPI::Group MPI::File::Get_group() const . MPI_FILE_GET_GROUP returns a duplicate of the group of the communicator used to open the file associated with fh. ... MPI_FILE_GET_AMODE(fh, amode) . ...

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• MPE_Draw_logic | PARALLEL.RU - Информационно-аналитический центр по
• Debugging for Nexus | PARALLEL.RU - Информационно-аналитический центр по
• MPI_Type_struct | PARALLEL.RU - Информационно-аналитический центр по

Internet Engineering Task Force (IETF) C. Daboo Request for Comments: 6868 Apple Updates: 5545, 6321, 6350, 6351 February 2013 Category: Standards Track ISSN: 2070-1721 Parameter Value Encoding in iCalendar and vCard Abstract This specification updates the data formats for iCalendar (RFC 5545) and vCard (RFC 6350) to allow parameter values to include certain characters forbidden by the existing specifications. Status of This Memo This is an Internet Standards Track document. ...

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• http://mirror.msu.net/pub/rfc-editor/rfc-ed-all/pdfrfc/rfc6868.txt.pdf
• http://mirror.msu.net/pub/rfc-editor/rfc-ed-all/pdfrfc/rfc795.txt.pdf
• http://mirror.msu.net/pub/rfc-editor/rfc-ed-all/rfc795.txt

Encode character sequences in "string" , by mapping characters (or sequences of characters) to an alternative character (or sequence of characters). ... String to encode . ... Parameter type not be used if old or new are given. old="tokenlist" . Comma-separated list of tokens to replace. ... Example: %SEARCH{ "%ENCODE{ "string with "quotes"" type="quotes" }%" noheader="on" }% When using old and new , be aware that the results of applying earlier tokens are not processed again using later tokens. ...

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• VarQUERYPARAMS < System < Foswiki

Expands the parameters to the query that was used to display the page. ... encoding="entity" . encoding="safe" . ... If this parameter is not given, "safe" encoding is performed which HTML entity encodes the characters '"<>% . ... safe : Encode characters '"<>% into HTML entities. (this is the default) . ... By default QUERYPARAMS encodes the characters '"<>% into HTML entities (same as encoding="safe") which is relatively safe. ... This topic: System > WebHome > Macros > VarQUERYPARAMS . ...

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• VarENCODE < System < Foswiki
• WebPreferences < PracticumV < Foswiki

... 2 from allpy import protein . ... 5 # Create sequences from string representation of sequence body . 6 sequence_1 = protein . ... 9 # Create alignment from sequences . 10 alignment = protein . ... 15 # For each sequence, print number of gaps and non-gaps in alignment . ... 19 for column in alignment . ... 24 print " %s : %s gaps, %s non-gaps" % ( row . ... 26 # Print number of gaps in each column . ... 29 column_gaps = 0 . 30 for sequence in alignment . ... 31 if sequence not in column : . ...

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• allpy: 1785e40b2a2d test/usecase1.py
• allpy: 80043822a41e allpy/fileio.py
• allpy: 80043822a41e test/usecase1.py