The Viral mRNA track shows alignments between viral mRNAs in GenBank and the SARS genome.
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.
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.
This track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.
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).