• Share
  • Email
  • Embed
  • Like
  • Save
  • Private Content
SNPDigger
 

SNPDigger

on

  • 804 views

a tool to identify SNPs from EST data

a tool to identify SNPs from EST data

Statistics

Views

Total Views
804
Views on SlideShare
796
Embed Views
8

Actions

Likes
0
Downloads
4
Comments
0

1 Embed 8

http://www.slideshare.net 8

Accessibility

Categories

Upload Details

Uploaded via as Adobe PDF

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

    SNPDigger SNPDigger Presentation Transcript

    • SNPDigger a tool to identify SNPs from EST data here used to be a funny © picture
    • 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 n space + n gap + n miss fva = 1 - N
    • ambiguous allele frequency n A + n G + nT + n C faa = fva - 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 used to be a funny © picture