2.6.6 Annotate & Predict Menu

This menu contains many tools for finding, predicting and annotating regions of interest in sequences and alignments. Plugins that involve sequence prediction and annotation will also appear in this menu when installed.

• Trim Ends: Trims vectors, primers and/or poor quality sequence. see section 10.2.2 .
• Transfer Annotations: Copies annotations to the reference and/or consensus sequence of an alignment or assembly. See section 8.2.3 .
• Annotate from Database: Annotates sequences with similar annotations from your database. See section 8.2.4
• Compare Annotations: Compares annotations across up to 3 annotation tracks or documents. See section 8.3 .
• Find ORFs: Finds all open reading frames in a sequence and annotates them
• Find Motifs: Searches for motifs in PROSITE format. Uses “fuzznuc” and “fuzzpro” from EMBOSS.
• Find CRISPR sites: Searches gRNA (CRISPR) sites and scores them based on on-target sequence features and off-target interactions. See section 15.1 .
• Analyze CRISPR editing results: Measures frequencies of common variants from your CRISPR experiment by mapping reads to the target sequence. See section 15.2 .
• Find Variations/SNPs: Finds variable positions in assemblies and alignments. See section 11.1.1 .
• Find Low/High Coverage: Finds regions with low or high read coverage in assemblies. See section 10.5 .
• Calculate Expression Levels: Calculates expression levels (RPKM, FPKM, TPM) for a single sample. See section 11.2 .
• Compare Expression Levels: Compares expression levels between two samples. See section 11.2 .