SNPDiggera tool to identify SNPs from EST data

here usedto be

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Goals

• work without genome data

• get «true» SNPs

• learn to find «true» SNPs by several features

candidate selection

• redundancy of mutations

• contig depth

• valid allele ratio

• ambiguous allele frequency

redundancy of mutations

fm = nmu / N

number of ESTs

number of mutations at locus

contig depth

numes = Sum(ESTs) in contig

valid allele ratio

fva = 1 -n space + n gap + n miss

N

ambiguous allele frequency

faa = fva -n A + n G + n T + n C

N

SNP identification

• mutation frequency

• residue conservation

• physical position

• mutation type

• alignment of neighbor profiles

• content of nearby alleles

training of filters

Evaluation

sensitivity = true positives / true positives + false negatives

specificity = true negatives / false positives + true negatives

Results

here usedto be

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