Guide for the Sequencing and Annotation Pages

(will be available soon)

Genome BLAST Graphics Overview

    To be able to see this page, you need a Java supporting browser. You have the option of choosing the genomic fragment by coordinates to see the graphics for a portion of the genome. The loading of the actual graphics page, which can be a little bit slow on some computers, is complete when you see the message "Applet NewContigView running" below the page.    

The blue bar at the top of the page represents the genome fragment and reveals its length in base pairs. Any ORFs identified using the program GLIMMER are shown as bright red arrows just below the blue bar; clicking on those arrows will lead to the GLIMMER output page.

    Below the genomic fragment are nucleotide and amino acid BLAST hits. Mousing over the colored arrows will show the first line of the BLAST output; clicking on them will lead to the associated NCBI BLAST alignment results page. The genome fragments are used for blastn searches, and individual ORFs and putative intergenic regions are used for blastp searches. Therefore, the blastn output will show the query coordinates with respect to the whole contig; and the blastp output will contain coordinates beginning at the first position of the ORF or intergenic region.