Indexing Similar DNA Sequences

FM-index of alignment with gaps

“…Thus, we continue to the next step (by skipping lines 6-12 and going to line 13). Otherwise (i.e., the size of (First, Last) is one or less), we compute Z ℓ as follows (lines [6][7][8][9][10][11][12]. Let Z m be the set of the string numbers in SAA[i]'s such that First ℓ+1 ≤ i ≤ Last ℓ+1 and B σ [i] = 1, and let Z c be the set of the string numbers in SAA[Last].…”

On-line String Matching in Highly Similar DNA Sequences

“…Huang et al [10] propose a solution which assumes that the input set of DNA sequences can be divided into common segments and non-common segments. Their solution assumes that every sequence di↵ers on m 0 positions from the reference and the designed data structure requires O(n log + m 0 log m 0 ) bits where n is the length of the reference sequence and is the size of the alphabet.…”

“…In [3] a solution based on the use of word level operations on bit vectors is presented. In similar way as [10], the general scheme of this technique store the entire of a reference sequence with only di↵erences between the remaining sequences. The authors build a su x array together with an Aho-Corasick automaton [1] to store identical segments and the non-common segments are converted into a binary word using 2 bits per base.…”

Haplotype-aware graph indexes

“…If the haplotypes are aligned, we can use the alignment to determine whether the mappings are equivalent. Text indexes can also take advantage of the alignment by storing shared substrings only once (Huang et al, 2010). The FM-index of alignment (Na et al, 2016(Na et al, , 2018 goes one step further by collapsing the multiple alignment into a directed acyclic graph (DAG), where each node is labeled by a sequence.…”