Chapter title |
AmpliSAS and AmpliHLA: Web Server Tools for MHC Typing of Non-Model Species and Human Using NGS Data
|
---|---|
Chapter number | 18 |
Book title |
HLA Typing
|
Published in |
Methods in molecular biology, January 2018
|
DOI | 10.1007/978-1-4939-8546-3_18 |
Pubmed ID | |
Book ISBNs |
978-1-4939-8545-6, 978-1-4939-8546-3
|
Authors |
Alvaro Sebastian, Magdalena Migalska, Aleksandra Biedrzycka, Sebastian, Alvaro, Migalska, Magdalena, Biedrzycka, Aleksandra |
Abstract |
AmpliSAS and AmpliHLA are web server tools for automatic genotyping of MHC genes from high-throughput sequencing data. AmpliSAS is designed specifically to analyze amplicon sequencing data from non-model species and it is able to perform de-novo genotyping without any previous knowledge of the reference alleles. AmpliHLA is a human-specific version, it performs HLA typing by comparing sequenced variants against human reference alleles from the IMGT/HLA database. Here we describe four genotyping protocols: the first two use amplicon sequencing data to genotype the MHC genes of a passerine bird and human respectively; the third and fourth present the HLA typing of a human cell line starting from RNA and exome sequencing data respectively. |
Mendeley readers
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Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 3 | 23% |
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Professor | 1 | 8% |
Lecturer | 1 | 8% |
Other | 1 | 8% |
Unknown | 1 | 8% |
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Unknown | 3 | 23% |