PairwiseAlignmentSmithWatermanOptionsPanelMainWidget Form Form Algorithm version: Algorithm version: Scoring matrix: Scoring matrix: Gap penalty Gap penalty Open: Open: Extension: Extension: QObject START SmithWatermanAlgorithmOPENCL::launch START SmithWatermanAlgorithmOPENCL::launch Kernel::setArg(%1) failed Kernel::setArg(%1) failed OPENCL: Running CL program OPENCL: Running CL program FINISH SmithWatermanAlgorithmOPENCL::launch FINISH SmithWatermanAlgorithmOPENCL::launch Starting cleanup OpenCL resources Starting cleanup OpenCL resources Finish cleanup OpenCL resources Finish cleanup OpenCL resources U2::GTest_SmithWatermnan ** ** , , .. .. U2::LocalWorkflow::SWPrompter unset unset translated translated Searches regions in each sequence from %1 similar to all pattern(s) taken from %2. Percent similarity between a sequence and a pattern is %3. Seaches in %4 of a %5 sequence. Outputs the regions found annotated as %6. Searches regions in each sequence from %1 similar to all pattern(s) taken from %2. Percent similarity between a sequence and a pattern is %3. Seaches in %4 of a %5 sequence. Outputs the regions found annotated as %6. U2::LocalWorkflow::SWWorker Annotate as Annotate as Algorithm Algorithm Input Data Input Data Pattern Annotations Pattern Annotations The regions found. The regions found. Name of the result annotations. Name of the result annotations. Min Score Min Score Minimal percent similarity between a sequence and a pattern. Minimal percent similarity between a sequence and a pattern. Version of the Smith-Waterman algorithm. You can use the optimized versions of the algorithm (SSE, CUDA and OpenCL) if your hardware supports these capabilities. Version of the Smith-Waterman algorithm. You can use the optimized versions of the algorithm (SSE, CUDA and OpenCL) if your hardware supports these capabilities. Search in Translation Search in Translation Translates a supplied nucleotide sequence to protein and searches in the translated sequence. Translates a supplied nucleotide sequence to protein and searches in the translated sequence. Substitution Matrix Substitution Matrix Describes the rate at which one character in a sequence changes to other character states over time. Describes the rate at which one character in a sequence changes to other character states over time. Filter Results Filter Results Specifies either to filter the intersected results or to return all the results. Specifies either to filter the intersected results or to return all the results. Gap Open Score Gap Open Score Penalty for opening a gap. Penalty for opening a gap. Gap Extension Score Gap Extension Score Penalty for extending a gap. Penalty for extending a gap. Use Pattern Names Use Pattern Names Use a pattern name as an annotation name. Use a pattern name as an annotation name. Qualifier name for pattern name Qualifier name for pattern name Name of qualifier in result annotations which is containing a pattern name. Name of qualifier in result annotations which is containing a pattern name. Smith-Waterman Search Smith-Waterman Search Searches regions in a sequence similar to a pattern sequence. Outputs a set of annotations. Under the hood is the well-known Smith-Waterman algorithm for performing local sequence alignment. Searches regions in a sequence similar to a pattern sequence. Outputs a set of annotations. Under the hood is the well-known Smith-Waterman algorithm for performing local sequence alignment. Auto Auto both strands both strands direct strand direct strand complementary strand complementary strand Null sequence supplied to Smith-Waterman: %1 Null sequence supplied to Smith-Waterman: %1 Incorrect value: pattern alphabet doesn't match sequence alphabet Incorrect value: pattern alphabet doesn't match sequence alphabet Pattern symbols not matching to alphabet Pattern symbols not matching to alphabet Incorrect value: score value must lay between 0 and 100 Incorrect value: score value must lay between 0 and 100 Incorrect value: filter name incorrect, default value used Incorrect value: filter name incorrect, default value used Incorrect value: result name is empty, default value used Incorrect value: result name is empty, default value used Could not find complement translation for %1, searching only direct strand Could not find complement translation for %1, searching only direct strand Invalid value: weight matrix with given name not exists Invalid value: weight matrix with given name not exists Pattern Data Pattern Data An input pattern sequence to search for. An input pattern sequence to search for. An input reference sequence to search in. An input reference sequence to search in. Null pattern supplied to Smith-Waterman: %1 Null pattern supplied to Smith-Waterman: %1 Can't find weight matrix name: '%1'! Can't find weight matrix name: '%1'! <empty> <empty> Wrong matrix selected. Alphabets do not match Wrong matrix selected. Alphabets do not match SmithWaterman algorithm not found: %1 SmithWaterman algorithm not found: %1 Incorrect value: search pattern, pattern is empty Incorrect value: search pattern, pattern is empty smith_waterman_task Smith waterman task Smith waterman subtasks Smith waterman subtasks Found %1 matches of pattern '%2' Found %1 matches of pattern '%2' U2::PairwiseAlignmentSmithWatermanTask Substitution matrix is empty Substitution matrix is empty Smith Waterman2 SequenceWalker Smith Waterman2 SequenceWalker Not enough memory on CUDA-enabled device. The space required is %1 bytes, but only %2 bytes are available. Device id: %3, device name: %4 Not enough memory on CUDA-enabled device. The space required is %1 bytes, but only %2 bytes are available. Device id: %3, device name: %4 The Smith-Waterman search allocates ~%1 bytes (%2 Mb) on CUDA device The Smith-Waterman search allocates ~%1 bytes (%2 Mb) on CUDA device %1 results found %1 results found U2::QDSWActor matches with at least %1 score matches with at least %1 score exact matches exact matches both strands both strands direct strand direct strand complement strand complement strand Finds pattern %1. Looks for %2 in %3. Finds pattern %1. Looks for %2 in %3. %1: percent of score out of bounds. %1: percent of score out of bounds. %1: incorrect result filter. %1: incorrect result filter. %1: pattern is empty. %1: pattern is empty. %1: can not find %2. %1: can not find %2. SSearch SSearch smith_waterman_task Smith-Waterman task Smith-Waterman Smith-Waterman Finds regions of similarity to the specified pattern in each input sequence (nucleotide or protein one). Under the hood is the well-known Smith-Waterman algorithm for performing local sequence alignment. Finds regions of similarity to the specified pattern in each input sequence (nucleotide or protein one). Under the hood is the well-known Smith-Waterman algorithm for performing local sequence alignment. Pattern Pattern A subsequence pattern to look for. A subsequence pattern to look for. Min score Min score The search stringency. The search stringency. Algorithm Algorithm Algorithm version. Algorithm version. Search in translation Search in translation Translate a supplied nucleotide sequence to protein then search in the translated sequence. Translate a supplied nucleotide sequence to protein then search in the translated sequence. Scoring matrix Scoring matrix The scoring matrix. The scoring matrix. Filter results Filter results Result filtering strategy. Result filtering strategy. Gap open score Gap open score Gap open score. Gap open score. Gap ext score Gap ext score Gap extension score. Gap extension score. Auto Auto U2::SWAlgorithmADVContext Find pattern [Smith-Waterman]... Find pattern [Smith-Waterman]... U2::SWAlgorithmPlugin Optimized Smith-Waterman Optimized Smith-Waterman Various implementations of Smith-Waterman algorithm Various implementations of Smith-Waterman algorithm U2::SWAlgorithmTask Smith Waterman2 SequenceWalker Smith Waterman2 SequenceWalker Not enough memory on CUDA-enabled device. The space required is %1 bytes, but only %2 bytes are available. Device id: %3, device name: %4 Not enough memory on CUDA-enabled device. The space required is %1 bytes, but only %2 bytes are available. Device id: %3, device name: %4 The Smith-Waterman search allocates ~%1 bytes (%2 Mb) on CUDA device The Smith-Waterman search allocates ~%1 bytes (%2 Mb) on CUDA device %1 results found %1 results found