Dear friends,
I've compared the two sequences and i ve got the locations of SNPs between the two sequences. for eg:
Sequence 1: ---------GCCTGCTGCTGGCCGGGCGGGGGACGGGG------------CGGGACCGGAGCCGGAGCTGCGGGGCGCACCGGCTAGA
sequence 2: CAGAGCTGCGCCTGCTGCTGGCCGGGCGGGGGACGGGG------------
o/p- 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109
now how can i distinguish which are synonymous and which are non synonymous SNPs from the given output? (NOTE: only for example i ve given two sequences with less nucleotides, but there are multiple sequences with thousands of nucleotide)
Answers from this previous question might be helpful: Synonymous And Non-Synonymous Snps