5.2.5 The Side Panel Controls

The panel to the right of the sequence viewer allows you to control what is displayed in the sequence viewer (e.g. translations, consensus sequences, graphs and annotations), displays sequence statistics, and provides functions for finding annotations, ORFs, and restriction sites on your sequences. A brief description of each tab is given below:

General Options

Contains the color options (see section 5.2.6 ), check-boxes to turn on and off main aspects of the sequence view and options for what to display as the name of each sequence.

Display

Contains options for displaying the translation and/or complement of a sequence, and turning off the original nucleotide sequence. See sections 5.4 and 5.5 for more information. This tab is not displayed for protein sequences.

Graphs

This option is visible when viewing nucleotide or protein sequences, chromatogram traces, sequence alignments or assemblies, and includes graphs for GC content, Identity, Coverage, and Quality. The graphs available for display depend on the type of sequence you are viewing. More detail on graphs for nucleotide and protein sequences is given in section 5.2.7 and for alignment and contig graphs is given in section 9.3.2 .

Annotations

On sequences containing annotations this tab will show a yellow arrow. It contains controls for turning on and off annotations of each type, customising the way each type is displayed, and filtering based on annotation name or type. See chapter 8.1 for more information on working with annotations.

Live Annotate and Predict

Contains real-time annotation generators such as Annotate from Database, Find ORFs and Transfer Annotations. To use one of these, turn on the check-box at the top of the generator you want to use and annotations will immediately be added to the sequence. You can then change settings for the generator and the annotations will change on the sequence in real-time as you do. If you want to save the annotations permanently on the sequence click Apply.

Restriction Analysis

This behaves similarly to the Live Annotate & Predict section above. Please refer to chapter 14 for full details.

Advanced

Contains advanced options for controlling the look of sequences and alignments, including wrapping, numbering, annotation placement and font sizes. See section 5.2.8 for more information.

Statistics

Displays statistics about the sequence or alignment currently being viewed, such as length, molecular weight and nucleotide, codon and amino acid frequencies. See section 5.2.9 for more information.