non-synonymous snp id
DESCRIPTION
"Large" data set project for Bioinformatics class identifying non-synonymous SNPs in sockeye salmonTRANSCRIPT
Additionally,
5’‐TCTAAAATGGGTGAC‐3
5’‐UCUAAAAUGGGUGAC‐3
1. UCU AAA AUG GGU GAC 2. . CUA AAA UGG GUG AC 3. . . UAA AAU GGG UGA C
dsDNA
RNA
6 possible RFs for dsDNA 3 possible RFs in each direction
1 sequence with 1 SNP
2 sequences, one for each SNP allele
Translate into AA sequence for all 6 reading frames
Determine RF with protein BLAST
Align AA sequences for RF with highest e‐value for each
locus
Identify non‐synonymous SNPs
2 sequences, one for each SNP allele
1 sequence with 1 SNP
http://www.ebi.ac.Tk/Tools/emboss/transeq/index.html?
276 sequences 84 sequences BLASTP
All 23 loci 18 loci
INPUT OUTPUT
Query Top Hit E‐value Scenario
AlleleLocus Reading frame
Only 1 reading frame had hits
Multiple reading frames had hits,1 had higher E‐value
17 synonymous SNPs (no change in AA)
1 non‐ synonymous SNP
SNP U1214: [A/C]
Gene: Sialytransferase
GO Terms
SNP Table AA difference
Create SNP Table Determine RF for ref seq via getORF
Import reading frame as GenBank format
Create new SNP table with AA difference