We have expanded the coloring and display options for mRNA tracks to include several ways to highlight gaps in alignments of query sequences (usually transcripts) to the genome, which frequently indicate a problem with the query sequence or with the genome assembly. Tracks may be colored by genomic, mRNA or nonsynonymous mRNA codons, mRNA bases, or different mRNA bases. Tracks may then be configured, through options on the description page, to display double horizontal lines at locations where both the genome and query sequence have an insertion and to display vertical lines of different colors to distinguish poly(A) tail insertions and insertions at the beginning, end or middle of the query (Figure 2). The new coloring scheme makes it easier to visually scan a region with hundreds of alignments and pick out regions of interest (Figure 3). The new display options are explained in detail on the mRNA track description pages.
