I am doing some work on a couple of gene SNPs that could be involved in susceptibility and resistance to infectious diseases.
Does anyone know any tools that could be used to detect potential SNPs hotspots in gene sequences?
snpdb at https://www.ncbi.nlm.nih.gov/snp/ is a good place to start looking for snps if you know the gene or sequences that you are interested in
Some tools you can have a look at:
Poly phred: http://droog.gs.washington.edu/polyphred/ It is an integrated program to identify heterozygous locations for SNP.
Poly Bayes: http://clavius.bc.edu/~marth/PolyBayes/ PolyBayes is a computer program for the automated analysis of SNP discovery in redundant DNA sequences.
QualitySNPng: https://www.bioinformatics.nl/QualitySNPng/ It is another software tool for detection of SNPs, designed in such a way that uses haplotype based scheme, it uses DNA sequences derived from next generation sequencing data. It performs on diploid as well as polyploidy species.
Hi. Some tools developed for NGS data analysis such as GATK tools, SNiPlay, and galaxy server can be employed for this goal.
in Bioinformatics you can easily analyzed your SNPs predisposition in any disease. there are many prediction tools like SIFT, POLYPHEN2, SNP&GO, PHD-SNP, PANTHER, PROVEAN and much more thats can characterized the SNPs into normal or deleterious effect
Hello,
There are several tools to detect SNPs and/or indel or CNVs on genes. You can use for example MAQ to Call SNPs but may also be used to align reads, VarScan to Identifies SNPs and indels but can be used with Roche/454 and Illumina reads, EBM to Identifies SNPs using an empirical Bayes mixture model and its implemented as R function, Syzygy to Detect SNPs and indels.
All the best
Gadji_M
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