High-quality reference alignments are essential if they are to be used as a starting point for further automatic alignment generation.
Belvu is used to analyse conservation patterns in multiple sequence alignments and to perform a combination of manual and automatic processing of the alignment. This is used to identify sequence that is not represented (or is misrepresented) and to quickly compare annotated gene models with transcriptional and protein evidence that putatively supports them.
Dotter is used to give a dot-plot representation of a particular pairwise alignment. Annotators use this for many reasons, including to check the quality of an alignment, to find missing/misaligned sequence and to identify splice sites and polyA sites and signals. Blixem displays the gene model positions and the match sequences aligned against the genomic reference sequence. Findingsīlixem is used by annotators to give a detailed view of the evidence for particular gene models. These tools were originally part of the AceDB genome database system but have been completely rewritten to make them generally available as a standalone package of greatly improved function. The SeqTools package provides three tools for viewing different types of sequence alignment: Blixem is a many-to-one browser of pairwise alignments, displaying multiple match sequences aligned against a single reference sequence Dotter provides a graphical dot-plot view of a single pairwise alignment and Belvu is a multiple sequence alignment viewer, editor, and phylogenetic tool.
Annotators need to be able to view sequence alignments in detail. Manual annotation is essential to create high-quality reference alignments and annotation.