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Fig. 1 | Algorithms for Molecular Biology

Fig. 1

From: HIA: a genome mapper using hybrid index-based sequence alignment

Fig. 1

Constructing the hybrid index. Panel a represents the procedure for constructing the hybrid index given Sequence = TATAGGCATGAGCCAC and q = 1. Construction proceeds as follows: first, convert the nucleotide symbols in sequence into the corresponding decimal values (I). Second, count each q-gram and store the counts in the HT (II-I). Third, set the beginning position of each q-gram based on the counts of q-grams (II-II). Fourth, store the positions of each q-gram in the SA such as (III). Finally, sort each q-gram range in the SA and finish hybrid index construction. The sizes of Sequence, SA, and HT are 16, 16, and 4q + 1=5, respectively. Panel b shows the constructed hybrid index

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