a tool to identify SNPs from EST data

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