By Mihai Pop, Hélène Touzet

This ebook constitutes the refereed court cases of the fifteenth overseas Workshop on Algorithms in Bioinformatics, WABI 2015, held in Atlanta, GA, united states, in September 2015. The 23 complete papers awarded have been rigorously reviewed and chosen from fifty six submissions. the chosen papers hide a variety of issues from networks to phylogenetic reviews, series and genome research, comparative genomics, and RNA structure.

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4 in the Appendix). Under GHOST’s NCF, WAVE is always superior to MI-GRAAL’s AS (G-W is better than G-M), and WAVE is superior to GHOST’s AS (G-W is better than G-G) with respect to two of the four measures (edge-based S3 and LCCS), while GHOST’s AS is superior (G-G is better than G-W) with respect to the other two measures (node-based NC and Exp-GO) (Figs. 4 in the Appendix). Hence, WAVE and GHOST’s AS are comparable overall. Again, WAVE in general works better under MI-GRAAL’s NCF than under GHOST’s, as M-W is overall superior to G-W.

Recall that a key novelty of WAVE is that while optimizing edge conservation (in addition to node conservation), WAVE weighs each conserved edge to favor aligning edges with highly NCF-similar end nodes. , M-W(U) and G-W(U)). As we will show, the edge-weighted versions are superior. , βn and βe ) on WAVE’s results. , equally favoring node and edge conservation, is superior to other parameter variations. Next, using the edge-weighted versions of WAVE with βn = 1 and βe = 1, we evaluate the five aligners (M-M, M-W, G-M, G-G, and G-W) against each other.

Best Alignments. Under MI-GRAAL’s NCF, WAVE is always superior (M-W is better than M-M) with respect to S3 , and it is almost always superior with respect to LCCS as well as Exp-GO (Figs. 5 in the Appendix). Hence, here WAVE is even more superior than for topological alignments only. Under GHOST’s NCF, WAVE is superior to MI-GRAAL’s AS (as G-W is better than G-M) in most cases for each of S3 and Exp-GO, and in some cases for LCCS. Also, here WAVE is overall superior to GHOST’s AS (G-W is better than G-G) with respect to Exp-GO but not with respect to S3 or LCCS (Figs.

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