Efficient association mapping from k-mers—An application in finding sex-specific sequences
| Autor: | Ibrahim Asadullah Tahmid, Atif Rahman, Zakaria Mehrab, Jaiaid Mobin |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Male
Microarray Computer science Genome-wide association study Genome Database and Informatics Methods Mathematical and Statistical Techniques Association mapping Principal Component Analysis Multidisciplinary Sex Chromosomes Bacterial Genomics Chromosome Biology Statistics Microbial Genetics Chromosome Mapping Eukaryota Genomics Sex specific Y Chromosomes Phenotype Physical Sciences Medicine Female Sequence Analysis Algorithms Research Article Bioinformatics Science Computational biology Microbial Genomics Research and Analysis Methods Microbiology Chromosomes Cnidaria Genetics Genome-Wide Association Studies Escherichia coli Animals Bacterial Genetics Humans Statistical Methods Molecular Biology Techniques Genotyping Molecular Biology Whole genome sequencing Whole Genome Sequencing Gene Mapping Organisms Biology and Life Sciences Computational Biology Bacteriology Human Genetics Cell Biology Sequence Analysis DNA Genome Analysis Invertebrates Multivariate Analysis Jellyfish Zoology Sequence Alignment Mathematics Ampicillin Resistance Genome Bacterial Reference genome Genome-Wide Association Study |
| Zdroj: | PLoS ONE PLoS ONE, Vol 16, Iss 1, p e0245058 (2021) |
| ISSN: | 1932-6203 |
| Popis: | Genome wide association studies (GWAS) attempt to map genotypes to phenotypes in organisms. This is typically performed by genotyping individuals using microarray or by aligning whole genome sequencing reads to a reference genome. Both approaches require knowledge of a reference genome which hinders their application to organisms with no or incomplete reference genomes. This caveat can be removed by using alignment-free association mapping methods based on k-mers from sequencing reads. Here we present an improved implementation of an alignment free association mapping method. The new implementation is faster and includes additional features to make it more flexible than the original implementation. We have tested our implementation on an E. Coli ampicillin resistance dataset and observe improvement in execution time over the original implementation while maintaining accuracy in results. We also demonstrate that the method can be applied to find sex specific sequences. |
| Databáze: | OpenAIRE |
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