## Description

The Viral mRNA track shows alignments between viral mRNAs in GenBank and the SARS genome.

## Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality.

## Methods

GenBank viral mRNAs were aligned against the genome using the blastz program. When a single mRNA aligned multiple places, the alignment having the highest base identity was found. Only those alignments having at least 60% base identity were kept. These alignments were converted into axt format and the resulting axts 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 were found by running a dynamic program over the kd-tree. Chains scoring below a certain threshold were discarded; the remaining chains are displayed in this track.

## Credits

This track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

## References

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.

Schwartz, S., Kent WJ., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. Human-mouse alignments with BLASTZ. Genome Res. 13(1), 103-107 (2003).