MatrixAndLogoWidget Form Form PWMBuildDialog Build Weight or Frequency Matrix Build Weight or Frequency Matrix Input file Input file ... ... Output file Output file Statistic options Statistic options Statistic type: Statistic type: Mononucleic Mononucleic Dinucleic Dinucleic Matrix options Matrix options Matrix type: Matrix type: Frequency matrix Frequency matrix Weight matrix Weight matrix Weight algorithm Weight algorithm Different weight algorithms uses different functions to build weight matrices. It allows us to get better precision on different data sets. Log-odds, NLG and Match algorithms are sensitive to input matrices with zero values, so some of them may not work on those matrices. Different weight algorithms uses different functions to build weight matrices. It allows us to get better precision on different data sets. Log-odds, NLG and Match algorithms are sensitive to input matrices with zero values, so some of them may not work on those matrices. PWMSearchDialog Weight Matrix Search Weight Matrix Search Matrix: Matrix: ... ... Minimal score Minimal score Score: Score: 85% 85% Load list Load list Save list Save list Load folder Load folder Build new matrix Build new matrix Weight algorithm Weight algorithm Strands Strands Both strands Both strands Direct strand Direct strand Range Range Matrix Matrix Search JASPAR Database Search JASPAR Database View matrix View matrix Reverse complement strand Reverse complement strand Algorithm Algorithm Clear list Clear list Strand Strand Score Score Clear results Clear results Save as annotations Save as annotations Status Status Minimum score to detect transcription factor binding site Minimum score to detect transcription factor binding site QObject Weight Matrix Weight Matrix Searches the sequence for transcription factor binding sites significantly similar to the specified weight matrix. Searches the sequence for transcription factor binding sites significantly similar to the specified weight matrix. Min score Min score Matrix Matrix Path to profile Path to profile Weight matrix Weight matrix Frequency matrix Frequency matrix SearchJASPARDatabase Search JASPAR Database Search JASPAR Database Name Name ID ID Class Class Family Family SetDefaultParametersDialog Set default parameters Set default parameters Weight algorithm Weight algorithm Score: Score: 85% 85% U2::LocalWorkflow::PFMatrixBuildPrompter For each MSA from %1, build Frequency Matrix. For each MSA from %1, build Frequency Matrix. U2::LocalWorkflow::PFMatrixBuildWorker Input alignment Input alignment Input multiple sequence alignment for building statistical model. Input multiple sequence alignment for building statistical model. Frequency matrix Frequency matrix Produced statistical model of specified TFBS data. Produced statistical model of specified TFBS data. Build Frequency Matrix Build Frequency Matrix Builds frequency matrix. Frequency matrices are used for probabilistic recognition of transcription factor binding sites. Builds frequency matrix. Frequency matrices are used for probabilistic recognition of transcription factor binding sites. Mononucleic Mononucleic Dinucleic Dinucleic U2::LocalWorkflow::PFMatrixConvertPrompter For each frequency matrix from %1, build weight matrix. For each frequency matrix from %1, build weight matrix. U2::LocalWorkflow::PFMatrixConvertWorker Weight matrix Weight matrix Frequency matrix to convert. Frequency matrix to convert. Frequency matrix Frequency matrix Produced statistical model of specified TFBS data. Produced statistical model of specified TFBS data. Convert Frequency Matrix Convert Frequency Matrix Converts frequency matrix to weight matrix. Weight matrices are used for probabilistic recognition of transcription factor binding sites. Converts frequency matrix to weight matrix. Weight matrices are used for probabilistic recognition of transcription factor binding sites. Mononucleic Mononucleic Dinucleic Dinucleic U2::LocalWorkflow::PFMatrixReadPrompter Read model(s) from %1. Read model(s) from %1. U2::LocalWorkflow::PFMatrixReader Loaded frequency matrix from %1 Loaded frequency matrix from %1 U2::LocalWorkflow::PFMatrixWritePrompter Save the profile(s) from %1 to %2. Save the profile(s) from %1 to %2. U2::LocalWorkflow::PFMatrixWriter Unspecified URL for writing frequency matrix Unspecified URL for writing frequency matrix Writing frequency matrix to %1 Writing frequency matrix to %1 U2::LocalWorkflow::PWMatrixBuildPrompter For each MSA from %1, build weight matrix. For each MSA from %1, build weight matrix. U2::LocalWorkflow::PWMatrixBuildWorker Input alignment Input alignment Input multiple sequence alignment for building statistical model. Input multiple sequence alignment for building statistical model. Weight matrix Weight matrix Produced statistical model of specified TFBS data. Produced statistical model of specified TFBS data. Weight algorithm Weight algorithm Matrix type Matrix type Dinucleic matrices are more detailed, while mononucleic one are more useful for small input data sets. Dinucleic matrices are more detailed, while mononucleic one are more useful for small input data sets. Build Weight Matrix Build Weight Matrix Builds weight matrix. Weight matrices are used for probabilistic recognition of transcription factor binding sites. Builds weight matrix. Weight matrices are used for probabilistic recognition of transcription factor binding sites. Mononucleic Mononucleic Dinucleic Dinucleic Different weight algorithms uses different functions to build weight matrices. It allows us to get better precision on different data sets. Log-odds, NLG and Match algorithms are sensitive to input matrices with zero values, so some of them may not work on those matrices. Different weight algorithms uses different functions to build weight matrices. It allows us to get better precision on different data sets. Log-odds, NLG and Match algorithms are sensitive to input matrices with zero values, so some of them may not work on those matrices. U2::LocalWorkflow::PWMatrixReadPrompter Read model(s) from %1. Read model(s) from %1. U2::LocalWorkflow::PWMatrixReader Loaded weight matrix from %1 Loaded weight matrix from %1 U2::LocalWorkflow::PWMatrixSearchPrompter unset unset For each sequence from %1, For each sequence from %1, with all profiles provided by %1, with all profiles provided by %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. U2::LocalWorkflow::PWMatrixSearchWorker Weight matrix Weight matrix Profile data to search with. Profile data to search with. Sequence Sequence Input nucleotide sequence to search in. Input nucleotide sequence to search in. Weight matrix annotations Weight matrix annotations Annotations marking found TFBS sites. Annotations marking found TFBS sites. Result annotation Result annotation Annotation name for marking found regions. Annotation name for marking found regions. Min score Min score Search for TFBS with Weight Matrix Search for TFBS with Weight Matrix Searches each input sequence for transcription factor binding sites significantly similar to specified weight matrices. 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 weight matrices. In case several profiles were supplied, searches with all profiles one by one and outputs merged set of annotations for each sequence. both strands both strands direct strand direct strand complement strand complement strand Find TFBS in %1 Find TFBS in %1 Bad sequence supplied to Weight Matrix Search: %1 Bad sequence supplied to Weight Matrix Search: %1 Found %1 TFBS Found %1 TFBS U2::LocalWorkflow::PWMatrixWritePrompter Save the profile(s) from %1 to %2. Save the profile(s) from %1 to %2. U2::LocalWorkflow::PWMatrixWriter Unspecified URL for writing weight matrix Unspecified URL for writing weight matrix Writing weight matrix to %1 Writing weight matrix to %1 U2::MatrixViewController Matrix viewer Matrix viewer U2::PFMatrixBuildTask Build Frequency Matrix Build Frequency Matrix Sequences in alignment have various lengths Sequences in alignment have various lengths Alignment is empty Alignment is empty Alignment is not nucleic Alignment is not nucleic Calculating frequencies of nucleotids Calculating frequencies of nucleotids U2::PFMatrixBuildToFileTask Build Weight Matrix Build Weight Matrix Input format error Input format error Loading alignment Loading alignment Wrong sequence alphabet Wrong sequence alphabet No alignments or sequences found No alignments or sequences found U2::PFMatrixFormat Position frequency matrix Position frequency matrix Position frequency matrix file. Position frequency matrix file. The file format is not PFM The file format is not PFM Zero length or corrupted model Maybe model data are not enough for selected algorithm Zero length or corrupted model Maybe model data are not enough for selected algorithm U2::PFMatrixReadTask Read Frequency Matrix Read Frequency Matrix U2::PFMatrixViewFactory Open multiple views Open multiple views PFM Viewer PFM Viewer U2::PFMatrixWriteTask Save position frequency matrix Save position frequency matrix U2::PWMBuildDialogController Select file with alignment Select file with alignment Wrong sequence alphabet Wrong sequence alphabet Select file to save frequency matrix to... Select file to save frequency matrix to... Frequency matrices Frequency matrices Weight matrices Weight matrices Select file to save weight matrix to... Select file to save weight matrix to... Overwrite existing file Overwrite existing file File with this name already exists. Do you want to write over this file? File with this name already exists. Do you want to write over this file? Illegal input file name Illegal input file name Illegal output file name Illegal output file name Counting frequency statistics Counting frequency statistics Hide Hide Cancel Cancel Could not detect the format of the file. Files must be in supported multiple alignment or sequence formats. Could not detect the format of the file. Files must be in supported multiple alignment or sequence formats. There are no sequences in the file. There are no sequences in the file. Build finished with errors: %1 Build finished with errors: %1 Build canceled Build canceled Build finished successfuly Build finished successfuly Start Start Close Close Running state %1 progress %2% Running state %1 progress %2% U2::PWMJASPARDialogController Select Select Cancel Cancel U2::PWMSearchDialogController Cancel Cancel Close Close Progress %1% Progress %1% Results found: %1. Results found: %1. Select file with frequency or weight matrix Select file with frequency or weight matrix Same model with same parameters already in the search queue Same model with same parameters already in the search queue Zero length or corrupted model Maybe model data is not enough for selected algorithm Zero length or corrupted model Maybe model data is not enough for selected algorithm Model not selected Model not selected Load file with list of matrices Load file with list of matrices CSV files (*.csv) CSV files (*.csv) Save file with list of matrices Save file with list of matrices Select folder with frequency or weight matrices Select folder with frequency or weight matrices Reverse complement strand Reverse complement strand Direct strand Direct strand Zero length or corrupted model Zero length or corrupted model Add to queue Add to queue Search Search Range is too small Range is too small U2::PWMatrixBuildTask Build Weight Matrix Build Weight Matrix Can't convert mononucleotide matrix to dinucleotide one Can't convert mononucleotide matrix to dinucleotide one Sequences in alignment have various lengths Sequences in alignment have various lengths Alignment is empty Alignment is empty Alignment is not nucleic Alignment is not nucleic U2::PWMatrixBuildToFileTask Build Weight Matrix Build Weight Matrix Input format error Input format error Loading alignment Loading alignment Wrong sequence alphabet Wrong sequence alphabet No alignments or sequences found No alignments or sequences found U2::PWMatrixFormat Position weight matrix Position weight matrix Position weight matrix file. Position weight matrix file. The file format is not PWM The file format is not PWM Zero length or corrupted model. Maybe model data are not enough for selected algorithm Zero length or corrupted model. Maybe model data are not enough for selected algorithm U2::PWMatrixReadTask Read Weight Matrix Read Weight Matrix U2::PWMatrixViewFactory Open multiple views Open multiple views PWM Viewer PWM Viewer U2::PWMatrixWriteTask Save weight matrix Save weight matrix U2::QDWMActor both strands both strands direct strand direct strand complement strand complement strand Searches TFBS with all profiles from %1 Recognizes sites with similarity %2, processes %3. Searches TFBS with all profiles from %1 Recognizes sites with similarity %2, processes %3. %1: sequence should be nucleic. %1: sequence should be nucleic. U2::ViewMatrixDialogController Close Close U2::WMQDTask Weight matrix query Weight matrix query U2::WeightMatrixADVContext Find TFBS with matrices... Find TFBS with matrices... U2::WeightMatrixIO Frequency and weight matrices Frequency and weight matrices Frequency matrices Frequency matrices Weight matrices Weight matrices Error parsing settings line %1 Error parsing settings line %1 Error parsing value %1 Error parsing value %1 Unexpected negative frequency value %1 Unexpected negative frequency value %1 Incorrect size of weight matrix: %1 Incorrect size of weight matrix: %1 Weight matrix Weight matrix Location Location Location hint for the target file. Location hint for the target file. Input weight matrix Input weight matrix Write Weight Matrix Write Weight Matrix Saves all input weight matrices to specified location. Saves all input weight matrices to specified location. Loaded weight matrices data. Loaded weight matrices data. Read Weight Matrix Read Weight Matrix Reads weight matrices from file(s). The files can be local or Internet URLs. Reads weight matrices from file(s). The files can be local or Internet URLs. Frequency matrix Frequency matrix Input frequency matrix Input frequency matrix Write Frequency Matrix Write Frequency Matrix Saves all input frequency matrices to specified location. Saves all input frequency matrices to specified location. Read Frequency Matrix Read Frequency Matrix Reads frequency matrices from file(s). The files can be local or Internet URLs. Reads frequency matrices from file(s). The files can be local or Internet URLs. U2::WeightMatrixPlugin Weight matrix Weight matrix Search for TFBS with weight matrices Search for TFBS with weight matrices Build weight matrix... Build weight matrix... U2::WeightMatrixSearchTask Weight matrix multiple search Weight matrix multiple search U2::WeightMatrixSingleSearchTask Weight matrix search Weight matrix search Weight matrix search parallel Weight matrix search parallel Internal error invalid psum: %1 Internal error invalid psum: %1 ViewMatrixDialog View Matrix View Matrix