SeqLab

Fall 1996 will see the Genetic Data Environment (GDE) merge with the Wisconsin Package graphic interface, formerly known as WPI. SeqLab, the new graphical interface, will combine GDE's easy single and multiple sequence editing tools, including cut, copy, and paste functions, with the wide range of sequence analysis tools that WPI provided. The GDE (Smith et al., CABIOS, 10(6):671-675) and WPI combination will also bring advanced sequence display features.

The new interface makes sequences the focal point of all analysis. Whenever possible, results will be represented in the context of the sequence or alignment.

Powerful sequence editing capabilities

• Enter new sequences, or edit existing ones, and then check them for accuracy using the checking mode.
• Align multiple sequences and group them to ensure that the alignment is maintained.
• Assign features to a sequence, allowing you to annotate your analysis.
• Highlight portions of your sequences or alignments with color for publication purposes.
• Select regions of a single sequence or of multiple sequences and analyze them with programs, such as PileUp or PlotSimilarity.
• Select regions of sequence based upon the feature table. This allows you to translation a set of exons for a gene, or to delete all introns.

Intuitive visualization capabilities

• Scaling is supported so that you can move from a global view of your sequence down to the nucleotide or peptide level.
• You can color your sequences based upon composition (similar amino acid codes sharing the same color) to aid in creating manual alignments. This is a very powerful way to view the quality of alignments, and recognize areas of high and low homology.
• You can view and manipulate feature tables. Feature tables can be represented as a schematic map of the sequence or as colored text. You can view alignments in this context as well, making feature comparison easy. Features are preserved even after a sequence is edited or aligned, and features can easily be added or removed.
• You can color you sequences based upon results from analysis functions. Search for patterns, or show conservation based upon PlotSimilarity, or consensus generation. Analysis functions can also return features to be added to a sequence's feature table, such as results from secondary structure prediction or motif searching.
• Coloring can also be used to show double stranded coverage in fragment assembly projects.
• WYSIWYG printing is available from all graphics and color modes.
• Monochrome displays can simulate color with patterns.