The Viral mRNA track shows alignments between viral mRNAs in Genbank and the SARS genome. Aligning regions (usually exons) are shown as black boxes connected by lines for gaps (spliced out introns usually). In full display, arrows on the introns indicate the direction of transcription.
Genbank Viral mRNAs are aligned against the genome using the BLASTZ program. When a single mRNA aligns in multiple places, the alignment having the highest base identity is found. Alignments must also have at least 60% base identity to be kept. The resulting alignments are converted into axt format and the resulting axts are fed into axtChain. AxtChain organizes all the alignments between a single viral mrna and the SARS genome into a group, and makes a kd-tree out of all the gapless subsections (blocks) of the alignments. Next, maximally scoring chains of these blocks are found by running a dynamic program over the kd-tree. Chains scoring below a threshold are discarded, and the remaining chains are displayed here.
The track filter can be used to change the color or include/exclude a subset of individual items within a track. This is helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter:
When you have finished configuring the filter, click the Submit button.
The $Organism mRNA track is produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.