ArticleBMC genetics2008
HaploSNPer: a web-based allele and SNP detection tool.
Article in BMC genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Article
- Single-Nucleotide Polymorphisms (SNP) Mining and Their Effect on the Tridimensional Protein Structure Prediction in a Set of Immunity-Related Expressed Sequence Tags (EST) in Atlantic Salmon (Frontiers in genetics · 2019Article
- SNP markers retrieval for a non-model species: a practical approach.BMC research notes · 2012Article
- SNP markers and their impact on plant breeding.International journal of plant genomics · 2012Article
- SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.BMC bioinformatics · 2011Article
- A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica.Plant physiology · 2010Article
- AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences.Algorithms for molecular biology : AMB · 2010Article
- In silico identification of new genetic variations as potential risk factors for Alzheimer's disease in a microarray-oriented simulation.Journal of molecular neuroscience : MN · 2009Article
- Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design.BMC bioinformatics · 2009Article
- Perl module and PISE wrappers for the integrated analysis of sequence data and SNP features.BMC research notes · 2009Article
- Functional genomics and SNP analysis of human genes encoding proline metabolic enzymes.Amino acids · 2008Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSingle nucleotide polymorphisms (SNPs) and small insertions or deletions (indels) are the most common type of polymorphisms and are frequently used for molecular marker development. Such markers have become very popular for all kinds of genetic analysis, including haplotype reconstruction. Haplotypes can be reconstructed for whole chromosomes but also for specific genes, based on the SNPs present. Haplotypes in the latter context represent the different alleles of a gene. The computational approach to SNP mining is becoming increasingly popular because of the continuously increasing number of sequences deposited in databases, which allows a more accurate identification of SNPs. Several software packages have been developed for SNP mining from databases. From these, QualitySNP is the only tool that combines SNP detection with the reconstruction of alleles, which results in a lower number of false positive SNPs and also works much faster than other programs. We have build a web-based SNP discovery and allele detection tool (HaploSNPer) based on QualitySNP.
resultsHaploSNPer is a flexible web-based tool for detecting SNPs and alleles in user-specified input sequences from both diploid and polyploid species. It includes BLAST for finding homologous sequences in public EST databases, CAP3 or PHRAP for aligning them, and QualitySNP for discovering reliable allelic sequences and SNPs. All possible and reliable alleles are detected by a mathematical algorithm using potential SNP information. Reliable SNPs are then identified based on the reconstructed alleles and on sequence redundancy.
conclusionThorough testing of HaploSNPer (and the underlying QualitySNP algorithm) has shown that EST information alone is sufficient for the identification of alleles and that reliable SNPs can be found efficiently. Furthermore, HaploSNPer supplies a user friendly interface for visualization of SNP and alleles. HaploSNPer is available from http://www.bioinformatics.nl/tools/haplosnper/.
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