Synonmous And Non Synonmous Snps

Question

[Payal]

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)

[Brad Chapman]

Answers from this previous question might be helpful: Synonymous And Non-Synonymous Snps

Answer 1

[Chris]

synonymous/non-syn. SNPs refer to protein coding regions. The latter alters the aminoacid while the first does not. So first of all you should be sure that the genomic sequences above are in exonic regions. Apart from that, a SNP is defined as such when it happens with a certain frequency in a population (not sure about the threshold though).

btw, I don't understand the dashes in your sequence. Does this represent an alignment?

[Elena]

ya -- represents the alignment

Answer 2

[Larry_Parnell]

Simply comparing two sequences of unknown quality makes it difficult to identify SNPs. If the 2 seqs are single reads from a high-throughput device, I would be hesitant to call any polymorphisms. If the above are high-quality and/or aligned to a reference genome, then you can begin to call SNPs and map them to a genome and its encoded genes.

So, with what you present above, you can perform a translated BLAST search (BLASTX) with seq as query against a protein database. The result should indicate if your seq and its SNPs fall into protein-coding region(s) and if so, if the SNP alters that protein sequence (non-synonymous) or not (synonymous).