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Alignment Viewer

 

Figure 4.  Alignment viewer result for target MAL8P1.335
(click for full-size image)

Figure 4 shows the figure generated by the alignment viewer for protein MAL8P1.335.  Each hairpin is represented by a light blue rectangle with our accession number drawn immediately to the side.  Numbers above the rectangle show the coordinate number of the first and last nucleotide in the hairpin. White rectangles within the hairpin represent the extreme left and right coordinates of the matches within the hairpin. Numbers below the white rectangles indicate the limits of the coordinates of the high scoring pairs (HSPs).  Plus / Plus strand matches are denoted by green lines while Plus / Minus strand matches are shown in red.  Vertical lines mark the exon boundaries of the protein.  The number(s) in parenthsis beside our accession is/are the minimum and maximum e-vaules associated with the set of HSPs in that hit.  If there is only one HSP, then only one value is reported.

From figure 4 we can see which regions, and even more specifically, which exons are most heavily targeted.  In the case of MAL8P1.335, half of the hairpin sequences matched in the third exon.  These diagrams allow us to distinguish possible low-complexity hits from group by means of the plus/plus and plus/minus strand.  Figure 5 shows an alignment that was generated using the same data, only with the low-complexity filter turned off.  The pattern of Plus / Plus and Plus / Minus matches seen in NC_004317-1504 is a likely sign of low-complexity matching.


Figure 5. Alignment viewer result for target PF14_0262 with
low-complexity filter turned off
(click for full-size image)
 
 

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