Approximate search of short patterns with high error rates using the 01⁎0 lossless seeds

Vroland, Christophe; Salson, Mikaël; Bini, Sbastien; Touzet, Hélène

doi:10.1016/j.jda.2016.03.002

Cited by 10 publications

(12 citation statements)

References 23 publications

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“…We performed our first set of comparisons with BWA [10], Yara [17], as well as an available implementation of the 01 * 0-filter scheme combined with dynamic programming (named Bwolo) [19] in the all-mapping mode. We did these comparisons for the edit distance only as all these tools work for edit distance.…”

Section: Towards a Full-fledged Alignermentioning

confidence: 99%

“…Moreover, imposing an all-mapping with maximum K errors in Bowtie2 in a way that its results are comparable to other tools is difficult. Bowtie2 settings used in [19] do not enforce this, and nonetheless, led to a very long running time for our data set (did not terminate in 13 hours). Consequently, we did not use Bowtie2 in this study.…”

Section: Towards a Full-fledged Alignermentioning

confidence: 99%

“…We would like to note that while BWA and Yara are standard read mapping tools for Illumina reads, Bwolo is interesting in the context of our approach. Vroland et al [19] presented this fast method for searching in an index by partitioning the read into K + 2 pieces for K errors and then exploiting the fact that the K + 2 pieces must contain the mismatch pattern 01 * 0. Their method searches for an occurrence of the 01 * 0 mismatch pattern in the read and then verifies the remaining pieces of the read partially in the index (they use a unidirectional index) and partially in the text via dynamic programming.…”

Section: Towards a Full-fledged Alignermentioning

confidence: 99%

“…Of course, we did not expect to be able to outperform full-fledged aligners for larger values of K, because for larger K and this read length, verification in index is too costly, especially if the number of successful verifications is low (in our case almost all reads occur only once in the genome). Although Vroland et al [19] raised the option of using a bidirectional index for verification, they only used in-text DP verification for the last pieces as they had only a unidirectional index at hand. Nevertheless, interestingly, for their data set (40bp, exactly 3 errors), pure index-based search using our optimal search schemes outperforms Bwolo by a factor of almost 1.5 (data not shown), so the read length matters.…”

Section: Towards a Full-fledged Alignermentioning

confidence: 99%

“…For the ASM problem for Hamming or edit distance, the existing algorithms all have exponential complexity in K (e.g. [5,19]), and are hence only suited for small K.…”

Section: Introductionmentioning

confidence: 99%

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Optimum Search Schemes for Approximate String Matching Using Bidirectional FM-Index

Kianfar

Pockrandt

Torkamandi

et al. 2018

Preprint

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Finding approximate occurrences of a pattern in a text using a full-text index is a central problem in bioinformatics and has been extensively researched. Bidirectional indices have opened new possibilities in this regard allowing the search to start from anywhere within the pattern and extend in both directions. In particular, use of search schemes (partitioning the pattern and searching the pieces in certain orders with given bounds on errors) can yield significant speed-ups. However, finding optimal search schemes is a difficult combinatorial optimization problem.Here for the first time, we propose a mixed integer program (MIP) capable to solve this optimization problem for Hamming distance with given number of pieces. Our experiments show that the optimal search schemes found by our MIP significantly improve the performance of search in bidirectional FM-index upon previous ad-hoc solutions. For example, approximate matching of 101-bp Illumina reads (with two errors) becomes 35 times faster than standard backtracking. Moreover, despite being performed purely in the index, the running time of search using our optimal schemes (for up to two errors) is comparable to the best stateof-the-art aligners, which benefit from combining search in index with in-text verification using dynamic programming. As a result, we anticipate a full-fledged aligner that employs an intelligent combination of search in the bidirectional FM-index using our optimal search schemes and in-text verification using dynamic programming that will outperform today's best aligners. The development of such an aligner, called FAMOUS (Fast Approximate string Matching using OptimUm search Schemes), is ongoing as our future work.

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Section: Towards a Full-fledged Alignermentioning

confidence: 99%

Section: Towards a Full-fledged Alignermentioning

confidence: 99%

Section: Towards a Full-fledged Alignermentioning

confidence: 99%

Section: Towards a Full-fledged Alignermentioning

confidence: 99%

“…For the ASM problem for Hamming or edit distance, the existing algorithms all have exponential complexity in K (e.g. [5,19]), and are hence only suited for small K.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations