Amplification bias in aDNA ...
Background: Repetitive microsatellite DNA forms a universal component of eukaryote genomes. These repeats provide well-recognized bioinformatics challenges, for instance when assembling genomes or aligning sequence data. Moreover, the specific biochemical properties of repetitive DNA can influence t...
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| Format: | Dataset |
| Language: | unknown |
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Norstore
2015
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| Online Access: | https://dx.doi.org/10.11582/2015.00013 https://archive.norstore.no/pages/public/datasetDetail.jsf?id=10.11582/2015.00013 |
| Summary: | Background: Repetitive microsatellite DNA forms a universal component of eukaryote genomes. These repeats provide well-recognized bioinformatics challenges, for instance when assembling genomes or aligning sequence data. Moreover, the specific biochemical properties of repetitive DNA can influence the outcome of laboratory protocols. These properties however, are not often considered when analyzing whole genome sequence (WGS) data. Results: Here we report that the Atlantic cod (Gadus morhua) genome contains an order of magnitude more dinucleotide repeats than the majority of vertebrate genomes, with over eight percent of its genome that can be classified as either AC or AG dinucleotide repeat. Furthermore, the abundance of these repeats can be inflated in ancient DNA (aDNA) WGS data generated from this species, in particular in poorly preserved samples. This repeat inflation is suppressed by a reduced number of amplification cycles and by the inclusion of manufactured dinucleotide repeat oligonucleotides ... : 2 gzip compressed data, from Unix, last modified: Mon Dec 8 21:38:03 2014, totaling ...... 18.22 MB 38 ASCII text, totaling ...... 6.94 GB 2 gzip compressed data, from Unix, last modified: Mon Dec 8 21:37:58 2014, totaling ...... 13.91 MB ... |
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