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Figure 7 | Algorithms for Molecular Biology

Figure 7

From: Fast local fragment chaining using sum-of-pair gap costs

Figure 7

Alignment of Human H/ACA snoRNA 77 and paralogous H/ACA snoRNA candidate retrieved by BLAST and clasp with sum-of-pair gap costs. Alignment of the Human H/ACA snoRNA 77 (SNORA77 in the snoRNABase) and a novel paralogous H/ACA snoRNA candidate retrieved by combined use of BLAST (options: -W 8 -e 1e+20 -F F) and clasp (sum-of-pair gap costs with , , fragment scores according to the length of the BLAST hit, and a minimal required chain score of 30). It shows a highly conserved H-box (blue rectangle) and ACA-motif (green rectangle) as well as high secondary structure conservation with two separate stem loop regions. Despite a sequence identity score of 70 reported by ClustalW, BLAST was capable to retrieve only 3 short regions, marked by red rectangles, none of which individually provides sufficient evidence of homology.

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