"Large" data set project for Bioinformatics class identifying non-synonymous SNPs in sockeye salmon

3. Additionally,

6. 5’‐TCTAAAATGGGTGAC‐3 dsDNA
5’‐UCUAAAAUGGGUGAC‐3 RNA
1. UCU AAA AUG GGU GAC 6 possible RFs for dsDNA
2. . CUA AAA UGG GUG AC 3 possible RFs in each direction
3. . . UAA AAU GGG UGA C

7. Translate into AA
1 sequence with 1 2 sequences, one for
sequence for all 6
SNP each SNP allele
reading frames
Align AA sequences
Determine RF with for RF with highest Identify non‐
protein BLAST e‐value for each synonymous SNPs
locus

8. 1 sequence with
1 SNP
2 sequences,
one for each
SNP allele

9. http://www.ebi.ac.Tk/Tools/emboss/transeq/index.html?

10. INPUT OUTPUT
BLASTP
276 sequences 84 sequences
All 23 loci 18 loci

11. Query Top Hit E‐value Scenario
Only 1 reading
frame had hits
Multiple reading
frames had hits,1
had higher E‐
value
Locus Reading frame
Allele

12. 17 synonymous SNPs (no change in AA)
1 non‐ synonymous SNP

13. GO Terms
SNP U1214: [A/C]
Gene: Sialytransferase

14. AA
SNP Table
difference
Determine RF for ref Import reading frame Create new SNP table
Create SNP Table
seq via getORF as GenBank format with AA difference