QObject Sitecon model Sitecon model SiteconBuildDialog Input alignment (nucleic) Input alignment (nucleic) ... ... Output model Output model Options Options Window is used to pick out the most important alignment region and is located at the center of the alignment. Must be: windows size is not greater than TFBS alignment length, recommended: windows size is not greater than 50 bp. Window is used to pick out the most important alignment region and is located at the center of the alignment. Must be: windows size is not greater than TFBS alignment length, recommended: windows size is not greater than 50 bp. Window size Window size bp bp Calibration random seed Calibration random seed Calibration sequence length Calibration sequence length 100 Kb 100 Kb 500 Kb 500 Kb 1 Mb 1 Mb 5 Mb 5 Mb Weight algorithm Weight algorithm Default status Default status None None Algorithm N2 Algorithm N2 Length of random synthetic sequences used to calibrate the profile. Should not be less than window size. Length of random synthetic sequences used to calibrate the profile. Should not be less than window size. SITECON Build SITECON Build The random seed, where <n> is a positive integer. You can use this option to generate reproducible results for different runs on the same data. The random seed, where <n> is a positive integer. You can use this option to generate reproducible results for different runs on the same data. Optional feature, in most cases applying no weight will fit. In some cases choosing algorithm 2 will increase the recognition quality. Optional feature, in most cases applying no weight will fit. In some cases choosing algorithm 2 will increase the recognition quality. SiteconSearchDialog SITECON Search SITECON Search File with model File with model ... ... Threshold Threshold Strands Strands Both strands Both strands Search in direct strand only Search in direct strand only Direct strand Direct strand Search in complement strand Search in complement strand Complement strand Complement strand Range Range Strand Strand PSUM PSUM First type error First type error Second type error Second type error Clear results Clear results Save as annotations Save as annotations Ready Ready Recognition quality threshold, should be less than 100%. Choosing too low threshold will lead to recognition of too many TFBS recognised with too low trustworthiness. Choosing too high threshold may result in no TFBS recognised. Recognition quality threshold, should be less than 100%. Choosing too low threshold will lead to recognition of too many TFBS recognised with too low trustworthiness. Choosing too high threshold may result in no TFBS recognised. Recognition quality percentage threshold. If you need to switch off this filter choose the lowest value. Recognition quality percentage threshold. If you need to switch off this filter choose the lowest value. U2::GTest_CompareSiteconModels Models not equal Models not equal U2::LocalWorkflow::SiteconBuildPrompter For each MSA from %1, build SITECON model. For each MSA from %1, build SITECON model. U2::LocalWorkflow::SiteconBuildWorker Build SITECON model Build SITECON model None Algorithm2 Random seed can not be less zero Random seed can not be less zero Calibration length can not be less zero Calibration length can not be less zero Window size can not be less zero Window size can not be less zero Built SITECON model from: %1 Built SITECON model from: %1 Input alignment Input alignment Sitecon model Sitecon model Origin Origin Window size, bp Window size Window size. Window size. Calibration length Calibration length Calibration length. Calibration length. Random seed Random seed Random seed. Random seed. Weight algorithm Weight algorithm Input multiple sequence alignment for building statistical model. Input multiple sequence alignment for building statistical model. Location of input alignment, used as optional hint for model description. Location of input alignment, used as optional hint for model description. Produced statistical model of specified TFBS data. Produced statistical model of specified TFBS data. Weight algorithm. Weight algorithm. Builds statistical profile for SITECON. The SITECON is a program for probabilistic recognition of transcription factor binding sites. Builds statistical profile for SITECON. The SITECON is a program for probabilistic recognition of transcription factor binding sites. U2::LocalWorkflow::SiteconReadPrompter Read model(s) from %1. Read model(s) from %1. U2::LocalWorkflow::SiteconReader Loaded SITECON model from %1 Loaded SITECON model from %1 U2::LocalWorkflow::SiteconSearchPrompter unset unset For each sequence from %1, For each sequence from %1, %1 search transcription factor binding sites (TFBS) %2. Recognize sites with similarity %3%, process %4. Output the list of found regions annotated as %5. %1 search transcription factor binding sites (TFBS) %2. Recognize sites with similarity %3%, process %4. Output the list of found regions annotated as %5. with all profiles provided by %1, with all profiles provided by %1, U2::LocalWorkflow::SiteconSearchWorker both strands both strands direct strand direct strand complement strand complement strand Sitecon Model Sitecon Model Sequence Sequence SITECON annotations SITECON annotations Result annotation Result annotation Recognition quality percentage threshold.If you need to switch off this filter choose the lowest value. Recognition quality percentage threshold.If you need to switch off this filter choose the lowest value. Alternative setting for filtering results, minimal value of Error type I. Note that all thresholds (by score, by err1 and by err2) are applied when filtering results.If you need to switch off this filter choose "0" value. Alternative setting for filtering results, minimal value of Error type I. Note that all thresholds (by score, by err1 and by err2) are applied when filtering results.If you need to switch off this filter choose "0" value. Alternative setting for filtering results, max value of Error type II. Note that all thresholds (by score, by err1 and by err2) are applied when filtering results.If you need to switch off this filter choose "1" value. Alternative setting for filtering results, max value of Error type II. Note that all thresholds (by score, by err1 and by err2) are applied when filtering results.If you need to switch off this filter choose "1" value. Search for TFBS with SITECON Search for TFBS with SITECON Min score can not be less 60% or more 100% Min score can not be less 60% or more 100% Min Err1 can not be less 0 or more 1 Min Err1 can not be less 0 or more 1 Max Err2 can not be less 0 or more 1 Max Err2 can not be less 0 or more 1 Search in strand can only be 0(both) or 1(direct) or -1(complement) Search in strand can only be 0(both) or 1(direct) or -1(complement) Find TFBS in %1 Find TFBS in %1 Bad sequence supplied to SiteconSearch: %1 Bad sequence supplied to SiteconSearch: %1 Found %1 TFBS Found %1 TFBS Profile data to search with. Profile data to search with. Input nucleotide sequence to search in. Input nucleotide sequence to search in. Annotations marking found TFBS sites. Annotations marking found TFBS sites. Annotation name for marking found regions. Annotation name for marking found regions. Searches each input sequence for transcription factor binding sites significantly similar to specified SITECON profiles. In case several profiles were supplied, searches with all profiles one by one and outputs merged set of annotations for each sequence. Searches each input sequence for transcription factor binding sites significantly similar to specified SITECON profiles. In case several profiles were supplied, searches with all profiles one by one and outputs merged set of annotations for each sequence. Min score Min score Min Err1 Min Err1 Max Err2 Max Err2 U2::LocalWorkflow::SiteconWritePrompter Save the profile(s) from %1 to %2. Save the profile(s) from %1 to %2. U2::LocalWorkflow::SiteconWriter Unspecified URL for writing Sitecon Unspecified URL for writing Sitecon Writing SITECON model to %1 Writing SITECON model to %1 U2::QDSiteconActor %1 %1 with profile provided by %1 %2</a> with profile provided by %1 %2</a> with all %1 %2 profiles</a> with all %1 %2 profiles</a> similarity %1% similarity %1% both strands both strands direct strand direct strand complement strand complement strand %1: incorrect sitecon model url(s) %1: incorrect sitecon model url(s) %1: min score can not be less 60% or more 100% %1: min score can not be less 60% or more 100% %1: min Err1 can not be less 0 or more 1 %1: min Err1 can not be less 0 or more 1 %1: max Err2 can not be less 0 or more 1 %1: max Err2 can not be less 0 or more 1 Sitecon SITECON Searches for transcription factor binding sites significantly similar to specified SITECON profiles. In case several profiles were supplied, searches with all profiles one by one and outputs merged set of annotations. Searches for transcription factor binding sites significantly similar to specified SITECON profiles. In case several profiles were supplied, searches with all profiles one by one and outputs merged set of annotations. Searches transcription factor binding sites (TFBS) %1. Recognize sites with %2, process %3. Searches transcription factor binding sites (TFBS) %1. Recognize sites with %2, process %3. Min score Min score Min Err1 Min Err1 Alternative setting for filtering results, minimal value of Error type I. Note that all thresholds (by score, by err1 and by err2) are applied when filtering results. Alternative setting for filtering results, minimal value of Error type I. Note that all thresholds (by score, by err1 and by err2) are applied when filtering results. Max Err2 Max Err2 Alternative setting for filtering results, max value of Error type II. Note that all thresholds (by score, by err1 and by err2) are applied when filtering results. Alternative setting for filtering results, max value of Error type II. Note that all thresholds (by score, by err1 and by err2) are applied when filtering results. Model Model Profile data to search with. Profile data to search with. U2::QDSiteconTask Sitecon Query SITECON Query U2::SiteconADVContext Find TFBS with SITECON... Find TFBS with SITECON... U2::SiteconBuildDialogController Build Build Cancel Cancel Illegal alignment file Illegal alignment file Illegal SITECON model file Illegal SITECON model file Error Error Starting calibration process Starting calibration process Hide Hide Build finished with error: %1 Build finished with error: %1 Build canceled Build canceled Build finished successfully Build finished successfully Close Close Running... State :%1 Progress: %2 Running... State :%1 Progress: %2 Sitecon models Sitecon models Select file with alignment Select file with alignment Select file to save model to... Select file to save model to... U2::SiteconBuildTask Build SITECON model Build SITECON model Alignment contains gaps Alignment contains gaps Alignment is empty Alignment is empty Alignment must have at least 2 sequences Alignment must have at least 2 sequences Alignment is not nucleic Alignment is not nucleic Window size is greater than alignment length Window size is greater than alignment length Calculating average and dispersion matrixes Calculating average and dispersion matrixes Calculating weights Calculating weights Calibrating first type error Calibrating first type error Calibrating second type error Calibrating second type error U2::SiteconBuildToFileTask Build SITECON model to file Build SITECON model to file Unknown alignment format Unknown alignment format Loading alignment Loading alignment No alignment found No alignment found U2::SiteconIO Not a sitecon model Not a sitecon model Error parsing settings, line %1 Error parsing settings, line %1 Error parsing window size: %1 Error parsing window size: %1 Error parsing calibration len: %1 Error parsing calibration len: %1 Error parsing RSEED: %1 Error parsing RSEED: %1 Error parsing number of sequence in original alignment: %1 Error parsing number of sequence in original alignment: %1 Error parsing in alignment %1 Error parsing in alignment %1 Error parsing %1 in line %2 Error parsing %1 in line %2 Error parsing in line %1 Error parsing in line %1 Error parsing %1 Error parsing %1 Illegal error %1 Illegal error %1 Error parsing file in line %1 Error parsing file in line %1 Number of 'average' and 'sdev' properties not matches Number of 'average' and 'sdev' properties not matches Number of 'average' and 'weight' properties not matches Number of 'average' and 'weight' properties not matches Property in file %1 is not the same as built-in: %2 Property in file %1 is not the same as built-in: %2 Error info in file is not complete Error info in file is not complete Model verification error Model verification error Illegal weight algorithm: %1 Illegal weight algorithm: %1 Model size not matched: %1, expected: %2 Model size not matched: %1, expected: %2 Duplicate property: %1 Duplicate property: %1 Property not recognized: %1 Property not recognized: %1 Sitecon model Sitecon model SITECON SITECON Sitecon models Sitecon models Input Sitecon model Input Sitecon model Saves all input SITECON profiles to specified location. Saves all input SITECON profiles to specified location. Write SITECON Model Write SITECON Model Loaded SITECON profile data. Loaded SITECON profile data. Reads SITECON profiles from file(s). The files can be local or Internet URLs. Reads SITECON profiles from file(s). The files can be local or Internet URLs. Read SITECON Model Read SITECON Model U2::SiteconPlugin SITECON SITECON SITECON - is a program package for revealing and analysis of conservative conformational and physicochemical properties in transcription factor binding sites sets. SITECON - is a program package for revealing and analysis of conservative conformational and physicochemical properties in transcription factor binding sites sets. Build SITECON model... Build SITECON model... U2::SiteconReadMultiTask Load sitecon models task Load sitecon models task U2::SiteconReadTask Read SITECON Model Read SITECON Model U2::SiteconSearchDialogController Search Search Cancel Cancel Close Close Progress: %1% Progress: %1% %1 results found %1 results found Select file with SITECON model Select file with SITECON model Error Error %1%, first type error %2, second type error %3 %1%, first type error %2, second type error %3 No model selected No model selected Range is too small Range is too small Error parsing minumum score Error parsing minumum score Complement strand Complement strand Direct strand Direct strand U2::SiteconSearchTask SITECON search SITECON search SITECON search parallel subtask SITECON search parallel subtask Internal error: invalid PSUM: %1 Internal error: invalid PSUM: %1 U2::SiteconWriteTask Save SITECON model Save SITECON model