CustomAutoAnnotationDialog Plasmid Auto Annotations Plasmid Auto Annotations Selected features Selected features Promoter Promoter Origin Origin Terminator Terminator Primer Primer Gene Gene Other features Other features Regulatory Regulatory FindAnnotationCollocationsDialog 1 1 2 2 Region size: Region size: Find Groups of Annotated Regions Find Groups of Annotated Regions Save regions as annotations Save regions as annotations Clear results Clear results Result strand Result strand Direct Direct Complement Complement Both Both Annotation must fit into region Annotation must fit into region U2::AnnotatorPlugin DNA Annotator DNA Annotator This plugin contains routines to manipulate and search DNA sequence annotations This plugin contains routines to manipulate and search DNA sequence annotations U2::AnnotatorViewContext Find annotated regions... Find annotated regions... Annotate plasmid... Annotate plasmid... Warning Warning No annotations found No annotations found U2::CollocationSearchTask Search for annotated regions Search for annotated regions U2::CollocationsDialogController Search Search Cancel Cancel <<click '+' button to add new annotation>> <<click '+' button to add new annotation>> Stop Stop Searching... found %1 regions. Progress: %2% Searching... found %1 regions. Progress: %2% Found %1 regions Found %1 regions Ready Ready Select annotation names to search Select annotation names to search No annotations left No annotations left U2::CustomAutoAnnotationDialog Annotate Annotate U2::CustomPatternAnnotationTask Custom pattern annotation Custom pattern annotation U2::CustomPatternAutoAnnotationUpdater Plasmid features Plasmid features U2::GeneByGeneReportTask Generating gene-by-gene approach report Generating gene-by-gene approach report U2::LocalWorkflow::CollocationPrompter sequence from %1 sequence from %1 set of annotations from %1 set of annotations from %1 For each %1 and %2, For each %1 and %2, For each %1%2, For each %1%2, Annotations themselves may not span beyond the region. Annotations themselves may not span beyond the region. %1 look if %2 annotations appear collocated within same region of length %3.%4 Output the list of found regions annotated as %5. %1 look if %2 annotations appear collocated within same region of length %3.%4 Output the list of found regions annotated as %5. U2::LocalWorkflow::CollocationWorker Group annotations Group annotations Create new annotations Create new annotations Result annotation Result annotation Name of the result annotations to mark found collocations. Name of the result annotations to mark found collocations. Group of annotations Group of annotations Region size Region size Effectively this is the maximum allowed distance between the interesting annotations in a group. Effectively this is the maximum allowed distance between the interesting annotations in a group. Must fit into region Must fit into region Whether the interesting annotations should entirely fit into the specified region to form a group. Whether the interesting annotations should entirely fit into the specified region to form a group. Result type Result type Copy original annotations or annotate found regions with new ones. Copy original annotations or annotate found regions with new ones. Include boundaries Include boundaries Include most left and most right boundary annotations regions into result or exclude them. Include most left and most right boundary annotations regions into result or exclude them. Collocation Search Collocation Search Copy original annotations Copy original annotations At least 2 annotations are required for collocation search. At least 2 annotations are required for collocation search. Annotated regions containing found collocations. Annotated regions containing found collocations. A list of annotation names to search. Found regions will contain all the named annotations. A list of annotation names to search. Found regions will contain all the named annotations. Finds groups of specified annotations in each supplied set of annotations, stores found regions as annotations. Finds groups of specified annotations in each supplied set of annotations, stores found regions as annotations. Input data Input data An input sequence and a set of annotations to search in. An input sequence and a set of annotations to search in. U2::LocalWorkflow::GeneByGeneReportPrompter unset unset For annotated genes from %1 build gene-by-gene approach report. For annotated genes from %1 build gene-by-gene approach report. With sequence identity of %1. With sequence identity of %1. Using %1 to compare gene and genome sequences. Using %1 to compare gene and genome sequences. Output result table to %1. Output result table to %1. If a report file already exists, %1 it If a report file already exists, %1 it U2::LocalWorkflow::GeneByGeneReportWorker Input annotations Input annotations Gene annotations. Gene annotations. Input sequences Input sequences Gene sequences. Gene sequences. Gene by gene report data. Gene by gene report data. Gene with similar regions to for report. Gene with similar regions to for report. Output file Output file File to store a report. File to store a report. Annotation name Annotation name Annotation name used to compare genes and reference genomes. Annotation name used to compare genes and reference genomes. Existing file Existing file If a target report already exists you should specify how to handle that. Merge two table in one. Overwrite or Rename existing file. If a target report already exists you should specify how to handle that. Merge two table in one. Overwrite or Rename existing file. Identity cutoff Identity cutoff Identity between gene sequence length and annotation length in per cent. BLAST identity (if specified) is checked after. Identity between gene sequence length and annotation length in per cent. BLAST identity (if specified) is checked after. Gene-by-gene Approach Report Gene-by-gene Approach Report Output a table of genes found in a reference sequence. Output a table of genes found in a reference sequence.