copMEM: finding maximal exact matches via sampling both genomes
نویسندگان
چکیده
منابع مشابه
essaMEM: finding maximal exact matches using enhanced sparse suffix arrays
We have developed essaMEM, a tool for finding maximal exact matches that can be used in genome comparison and read mapping. essaMEM enhances an existing sparse suffix array implementation with a sparse child array. Tests indicate that the enhanced algorithm for finding maximal exact matches is much faster, while maintaining the same memory footprint. In this way, sparse suffix arrays remain com...
متن کاملComparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches
Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller ...
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We have developed a tool for rapidly determining the number of exact matches of any word within large, internally repetitive genomes or sets of genomes. Thus we can readily annotate any sequence, including the entire human genome, with the counts of its constituent words. We create a Burrows-Wheeler transform of the genome, which together with auxiliary data structures facilitating counting, ca...
متن کاملE-MEM: efficient computation of maximal exact matches for very large genomes
MOTIVATION Alignment of similar whole genomes is often performed using anchors given by the maximal exact matches (MEMs) between their sequences. In spite of significant amount of research on this problem, the computation of MEMs for large genomes remains a challenging problem. The leading current algorithms employ full text indexes, the sparse suffix array giving the best results. Still, their...
متن کاملA practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays
MOTIVATION High-throughput sequencing technologies place ever increasing demands on existing algorithms for sequence analysis. Algorithms for computing maximal exact matches (MEMs) between sequences appear in two contexts where high-throughput sequencing will vastly increase the volume of sequence data: (i) seeding alignments of high-throughput reads for genome assembly and (ii) designating anc...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2018
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bty670