Figure 1.

Global view of the PowerBLAST results in Chromoscope. The query sequence 214K23.01169 is a P1-derived artificial chromosome (PAC) clone in the 900-kb region of human chromosome 13 that contains the BRCA2 gene. The sequence was obtained from the web site of the Washington University Genome Sequencing Center (http://genome.wustl.edu) and at the time of retrieval these data were in “phase 2” of finishing. The shaded regions in the query sequence indicate the locations of repeat regions identified by PowerBLAST. The results from BLASTN and BLASTX are grouped into separate rectangles. Each line within the rectangle represents one alignment, and if parts of the matching sequence align to more than one region, the lines are shown in color (this situation occurs when an mRNA sequence is split into its component exons upon alignment with its gene). There are three clusters of alignments. The first is from 500 to 1000 nucleotides (between 0 and 1K on the scaled diagram), the second from ∼3K to 5K nucleotides, and the last from 8.5K to 11K nucleotides. In all of the regions, both BLASTN and BLASTX hits were found. The first and second cluster code for the last four exons of the BRCA2 gene (GenBank accession no. Z74739), whereas the third cluster shows high similarity to a 56-kD interferon-induced protein (SwissProt P09914) and its mRNA (GenBank accession no. M24594).