RF: A method for filtering short reads with tandem repeats for genome mapping
نویسندگان
چکیده
منابع مشابه
Resolving complex tandem repeats with long reads
MOTIVATION Resolving tandemly repeated genomic sequences is a necessary step in improving our understanding of the human genome. Short tandem repeats (TRs), or microsatellites, are often used as molecular markers in genetics, and clinically, variation in microsatellites can lead to genetic disorders like Huntington's diseases. Accurately resolving repeats, and in particular TRs, remains a chall...
متن کاملSystematic Profiling of Short Tandem Repeats in the Cattle Genome
Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2–6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in d...
متن کاملFiltering Tandem Repeats in DNA Sequences
A tandem repeat is a sequence of two or more contiguous, approximate copies of a pattern. Tandem repeats occur in the genomes of both eukaryotic and prokaryotic organisms. They are important in numerous fields including disease diagnosis, mapping studies, human identity testing (DNA fingerprinting), sequence homology, and population studies. Although tandem repeats have been used by biologists ...
متن کاملCharacterisation of short tandem repeats for genotyping Mycobacterium leprae.
OBJECTIVE Establish a typing system for Mycobacterium leprae based on polymorphic DNA structures known as short tandem repeats (STR). DESIGN Assess 16 polymorphic STR for sensitivity, specificity and reproducibility in standard assays using reference strains of M. leprae. RESULTS Primers for 16 STR loci were selected based on PCR product size and for their ability to sequence each STR locus...
متن کاملAn efficient algorithm for finding short approximate non-tandem repeats
We study the problem of approximate non-tandem repeat extraction. Given a long subject string S of length N over a finite alphabet Sigma and a threshold D, we would like to find all short substrings of S of length P that repeat with at most D differences, i.e., insertions, deletions, and mismatches. We give a careful theoretical characterization of the set of seeds (i.e., some maximal exact rep...
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ژورنال
عنوان ژورنال: Genomics
سال: 2013
ISSN: 0888-7543
DOI: 10.1016/j.ygeno.2013.03.002