The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.
Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data
Open accessAbstract
We have developed a computer based method to identify candidate single nucleotide polymorphisms (SNPs) and small insertions/deletions from expressed sequence tag data. Using a redundancy-based approach, valid SNPs are distinguished from erroneous sequence by their representation multiple times in an alignment of sequence reads. A second measure of validity was also calculated based on the cosegregation of the SNP pattern between multiple SNP loci in an alignment. The utility of this method was demonstrated by applying it to 102,551 maize (Zea mays) expressed sequence tag sequences. A total of 14,832 candidate polymorphisms were identified with an SNP redundancy score of two or greater. Segregation of these SNPs with haplotype indicates that candidate SNPs with high redundancy and cosegregation confidence scores are likely to represent true SNPs. This was confirmed by validation of 264 candidate SNPs from 27 loci, with a range of redundancy and cosegregation scores, in four inbred maize lines. The SNP transition/transversion ratio and insertion/deletion size frequencies correspond to those observed by direct sequencing methods of SNP discovery and suggest that the majority of predicted SNPs and insertion/deletions identified using this approach represent true genetic variation in maize.
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A general approach to single-nucleotide polymorphism discovery
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Mining SNPs From EST Databases
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Cited by
An overview of molecular marker methods for plants
Semagn, K., Bjørnstad, Å., & Ndjiondjop, M. (2006) · AFRICAN JOURNAL OF BIOTECHNOLOGY · doi:10.5897/ajb2006.000-5110 · Cited by 469
SNP discovery via 454 transcriptome sequencing
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Tissue Culture-Induced Heritable Genomic Variation in Rice, and Their Phenotypic Implications
Zhang, D., Wang, Z., Wang, N., Gao, Y., Liu, Y., Wu, Y., Bai, Y., Zhang, Z., Lin, X., Dong, Y., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0096879 · Cited by 90
Metadata
- Authors
- Batley, J., Barker, G., O'Sullivan, H., Edwards, K. J., & Edwards, D.
- Venue
- Plant Physiology
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-05-01
- Volume
- 132
- Issue
- 1
- Pages
- 84-91
- ISSN
- 0032-0889 (ISSN-L)
- 1532-2548
- OpenAlex
- W2124861078
- Cited by
- 294
- References
- 25
- FWCI
- 8.04
- Type
- journal article
- Language
- en
- Open access
- green
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- Batley, J., Barker, G., O'Sullivan, H., Edwards, K. J., & Edwards, D. (2003). Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data. Plant Physiology. https://doi.org/10.1104/pp.102.019422
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
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