Comparing the graphical representations of BLAST alignment by the BLASTGrabber, BlastViewer and JAMBLAST programs. A) HSP alignments from both “Fibronectin-3 motif” and “I-Set motif” queries aligned against the “D1YSG0_DROME Bent” protein sequence in the BLASTGrabber program. Triggered by positioning the mouse over it, details for the first HSP are displayed. Based on a selected HSP attribute such as e-values or bit scores, the HSP representations can be colour-coded as a heat map (not shown because this would hide the HSP query names) B) HSP for the “Fibronectin-3 motif” query aligned against same protein in the BlastViewer program. In this program, HSPs for multiple queries cannot be displayed in the same graphical representation. The HSP overlaps are colour-coded (purple, green and black) so as to reflect significance categories. C) The same HSPs (“Fibronectin-3 motif” vs. “D1YSG0_DROME Bent”) as displayed by the JAMBLAST program. Again, alignments from multiple queries cannot be displayed along the same sequence.