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Published on: May 22, 2018
HaploSNPer: a web-based allele and SNP detection tool.
Jifeng Tang1, Jack A M Leunissen, Roeland E Voorrips
1Laboratory of Bioinformatics, Wageningen University, PO Box 8128, 6700 ET Wageningen, The Netherlands. jack.leunissen@wur.nl.
HaploSNPer efficiently identifies single nucleotide polymorphisms (SNPs) and gene alleles using EST data. This web-based tool aids genetic analysis by accurately detecting variations and reconstructing alleles, improving molecular marker development.
Area of Science:
- Bioinformatics
- Computational Biology
- Genetics
Background:
- Single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels) are common genetic variations used for molecular marker development.
- Haplotype reconstruction, crucial for genetic analysis, relies on identifying SNPs within chromosomes or genes to define alleles.
- Computational SNP mining is increasingly vital due to vast sequence databases, enabling more accurate SNP identification.
Purpose of the Study:
- To develop HaploSNPer, a web-based tool for SNP discovery and allele detection, building upon the QualitySNP algorithm.
- To provide a user-friendly platform for identifying reliable SNPs and reconstructing gene alleles from sequence data.
Main Methods:
- HaploSNPer integrates BLAST for sequence homology searches, CAP3/PHRAP for sequence alignment, and QualitySNP for SNP and allele detection.
- A mathematical algorithm is employed to identify all possible and reliable alleles using potential SNP information.
- Reliable SNPs are determined based on reconstructed alleles and sequence redundancy, supporting both diploid and polyploid species.
Main Results:
- HaploSNPer successfully detects SNPs and alleles in user-specified sequences.
- The tool demonstrates efficiency in identifying reliable SNPs and reconstructing alleles.
- EST information alone proved sufficient for accurate allele identification and reliable SNP discovery.
Conclusions:
- HaploSNPer, powered by QualitySNP, efficiently identifies alleles and reliable SNPs using EST data.
- The tool offers a user-friendly interface for visualizing SNPs and alleles.
- HaploSNPer is accessible online for researchers in genetic analysis and molecular marker development.
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