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a tool to identify SNPs from EST data
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SNPDigger
1.
SNPDigger a tool to
identify SNPs from EST data here used to be a funny © picture
2.
Goals • work without
genome data • get «true» SNPs • learn to find «true» SNPs by several features
3.
candidate selection • redundancy
of mutations • contig depth • valid allele ratio • ambiguous allele frequency
4.
redundancy of
mutations fm = nmu / N number of ESTs number of mutations at locus
5.
contig depth numes =
Sum(ESTs) in contig
6.
valid allele ratio
n space + n gap + n miss fva = 1 - N
7.
ambiguous allele
frequency n A + n G + nT + n C faa = fva - N
8.
SNP identification • mutation
frequency • residue conservation • physical position • mutation type • alignment of neighbor profiles • content of nearby alleles
9.
training of filters
10.
Evaluation sensitivity = true
positives / true positives + false negatives specificity = true negatives / false positives + true negatives
11.
Results here used
to be a funny © picture
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