Unified View of Backward Backtracking in Short Read Mapping

Mäkinen, Veli; Välimäki, Niko; Laaksonen, Antti; Katainen, Riku

doi:10.1007/978-3-642-12476-1_13

Cited by 12 publications

(11 citation statements)

References 26 publications

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“…The pseudocode of a backtracking aware backward search that finds all k -mismatch occurrences of P in T is given in Algorithm k MISMATCHSEARCH [83]. …”

Section: Bwt-based Methodsmentioning

confidence: 99%

“…The worst case running time of k MISMATCHSEARCH is

scriptO ({| \sum |}^{k} m^{k + 1})

[83]. To further improve their practical performance, Bowtie [60] and BWA [63] invest some additional memory to not only build the FM index for the genome T , called the forward index, but also for the reverse (not complemented) genomic sequence T r = t n t n− 1 ⋯ t 1 , called the reverse or mirror index.…”

Section: Bwt-based Methodsmentioning

confidence: 99%

“…BWA uses the reverse index to precompute for each prefix P [1, i ] of a given read P the minimum number of parts D [ i ] into which P [l, i ] has to be broken into such that each part occurs at least once in genome T (exactly) [83]. Array D can be computed in time linear in the read length through a backward search of the reverse read in the reverse FM index, increasing the current entry of D by one every time range [ sp,ep ] becomes empty.…”

Section: Bwt-based Methodsmentioning

confidence: 99%

“…In [83] the pruning heuristics introduced in Sections III-C2a and III-C2b were experimentally evaluated on ChIP-seq data taken from [111] comprising 10,000 36 bp long reads. For a varying number of mismatches k these heuristics were compared against the suffix filter [48], a state of the art filtering algorithm (see Section II) developed for the approximate string matching problem.…”

Section: Bwt-based Methodsmentioning

confidence: 99%

“…The case sensitive backtracking strategy implemented by Bowtie slightly outperformed the suffix filter in terms of search time per read, when either the best, or all occurrences were located. A novel pruning heuristic proposed in [83] that combines suffix filter and case sensitive backtracking was superior in speed, at the cost of a significantly higher space consumption.…”

Section: Bwt-based Methodsmentioning

confidence: 99%

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Short Read Mapping: An Algorithmic Tour

Canzar

Salzberg

2017

Proc. IEEE

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Ultra-high-throughput next-generation sequencing (NGS) technology allows us to determine the sequence of nucleotides of many millions of DNA molecules in parallel. Accompanied by a dramatic reduction in cost since its introduction in 2004, NGS technology has provided a new way of addressing a wide range of biological and biomedical questions, from the study of human genetic disease to the analysis of gene expression, protein-DNA interactions, and patterns of DNA methylation. The data generated by NGS instruments comprise huge numbers of very short DNA sequences, or ’reads’, that carry little information by themselves. These reads therefore have to be pieced together by well-engineered algorithms to reconstruct biologically meaningful measurments, such as the level of expression of a gene. To solve this complex, high-dimensional puzzle, reads must be mapped back to a reference genome to determine their origin Due to sequencing errors and to genuine differences between the reference genome and the individual being sequenced, this mapping process must be tolerant of mismatches, insertions, and deletions. Although optimal alignment algorithms to solve this problem have long been available, the practical requirements of aligning hundreds of millions of short reads to the 3 billion base pair long human genome have stimulated the development of new, more efficient methods, which today are used routinely throughout the world for the analysis of NGS data.

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“…The pseudocode of a backtracking aware backward search that finds all k -mismatch occurrences of P in T is given in Algorithm k MISMATCHSEARCH [83]. …”

Section: Bwt-based Methodsmentioning

confidence: 99%

“…The worst case running time of k MISMATCHSEARCH is

scriptO ({| \sum |}^{k} m^{k + 1})

Section: Bwt-based Methodsmentioning

confidence: 99%

Section: Bwt-based Methodsmentioning

confidence: 99%

Section: Bwt-based Methodsmentioning

confidence: 99%

Section: Bwt-based Methodsmentioning

confidence: 99%

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Short Read Mapping: An Algorithmic Tour

Canzar

Salzberg

2017

Proc. IEEE

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Indexing Finite Language Representation of Population Genotypes

Sirén

Välimäki

Mäkinen

2011

Lecture Notes in Computer Science

Self Cite

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Abstract. With the recent advances in DNA sequencing, it is now possible to have complete genomes of individuals sequenced and assembled. This rich and focused genotype information can be used to do different population-wide studies, now first time directly on whole genome level. We propose a way to index population genotype information together with the complete genome sequence, so that one can use the index to efficiently align a given sequence to the genome with all plausible genotype recombinations taken into account. This is achieved through converting a multiple alignment of individual genomes into a finite automaton recognizing all strings that can be read from the alignment by switching the sequence at any time. The finite automaton is indexed with an extension of Burrows-Wheeler transform to allow pattern search inside the plausible recombinant sequences. The size of the index stays limited, because of the high similarity of individual genomes. The index finds applications in variation calling and in primer design. On a variation calling experiment, we found about 1.0% of matches to novel recombinants just with exact matching, and up to 2.4% with approximate matching.

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