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 .
• Annotate from Database: Annotates sequences with similar annotations from your database. See section 8.2.3
• Find ORFs: Finds all open reading frames in a sequence and annotates them
• Search for Motifs: Searches for motifs in PROSITE format. Uses “fuzznuc” and “fuzzpro” from EMBOSS.
• 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 .
• Transfer Annotations: Copies annotations to the reference and/or consensus sequence of an alignment or assembly. See section 8.2.3 .
• Compare Annotations: Compares annotations across up to 3 annotation tracks or documents. See section 8.3 .