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How to find the SNPs which are from frequent to rare using Perl programming?

How can i find out what are the changes(SNPs)in the sequence which are from frequent to rare( frequent codon to rare codon)? what will be the concept behind writing a program?

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  1. >gi|157266327|ref|NM_000465.2| Homo sapiens BRCA1 associated RING domain 1 (BARD1), mRNA
  2. CCTCTGGCGGCCCGCCGTCCCAGACGCGGGAAGAGCTTGGCCGGTTTCGAGTCGCTGGCCTGCAGCTTCCCTGTGGTTTCCCGAGGCTTCCTTGCTTCCCGCTCTGCGAGGAGCCTTTCATCCGAAGGCGGGACGATGCCGGATAATCGGCAGCCGAGGAACCGGCAGCCGAGGATCCGCTCCGGGAACGAGCCTCGTTCCGCGCCCGCCATGGAACCGGATGGTCGCGGTGCCTGGGCCCACAGTCGCGCCGCGCTCGACCGCCTGGAGAAGCTGCTGCGCTGCTCGCGTTGTACTAACATTCTGAGAGAGCCTGTGTGTTTAGGAGGATGTGAGCACATCTTCTGTAGTAATTGTGTAAGTGACTGCATTGGAACTGGATGTCCAGTGTGTTACACCCCGGCCTGGATACAAGACTTGAAGATAAATAGACAACTGGACAGCATGATTCAACTTTGTAGTAAGCTTCGAAATTTGCTACATGACAATGAGCTGTCAGATTTGAAAGAAGATAAACCTAGGAAAAGTTTGTTTAATGATGCAGGAAACAAGAAGAATTCAATTAAAATGTGGTTTAGCCCTCGAAGTAAGAAAGTCAGATATGTTGTGAGTAAAGCTTCAGTGCAAACCCAGCCTGCAATAAAAAAAGATGCAAGTGCTCAGCAAGACTCATATGAATTTGTTTCCCCAAGTCCTCCTGCAGATGTTTCTGAGAGGGCTAAAAAGGCTTCTGCAAGATCTGGAAAAAAGCAAAAAAAGAAAACTTTAGCTGAAATCAACCAAAAATGGAATTTAGAGGCAGAAAAAGAAGATGGTGAATTTGACTCCAAAGAGGAATCTAAGCAAAAGCTGGTATCCTTCTGTAGCCAACCATCTGTTATCTCCAGTCCTCAGATAAATGGTGAAATAGACTTACTAGCAAGTGGCTCCTTGACAGAATCTGAATGTTTTGGAAGTTTAACTGAAGTCTCTTTACCATTGGCTGAGCAAATAGAGTCTCCAGACACTAAGAGCAGGAATGAAGTAGTGACTCCTGAGAAGGTCTGCAAAAATTATCTTACATCTAAGAAATCTTTGCCATTAGAAAATAATGGAAAACGTGGCCATCACAATAGACTTTCCAGTCCCATTTCTAAGAGATGTAGAACCAGCATTCTGAGCACCAGTGGAGATTTTGTTAAGCAAACGGTGCCCTCAGAAAATATACCATTGCCTGAATGTTCTTCACCACCTTCATGCAAACGTAAAGTTGGTGGTACATCAGGGAGGAAAAACAGTAACATGTCCGATGAATTCATTAGTCTTTCACCAGGTACACCACCTTCTACATTAAGTAGTTCAAGTTACAGGCGAGTGATGTCTAGTCCCTCAGCAATGAAGCTGTTGCCCAATATGGCTGTGAAAAGAAATCATAGAGGAGAGACTTTGCTCCATATTGCTTCTATTAAGGGCGACATACCTTCTGTTGAATACCTTTTACAAAATGGAAGTGATCCAAATGTTAAAGACCATGCTGGATGGACACCATTGCATGAAGCTTGCAATCATGGGCACCTGAAGGTAGTGGAATTATTGCTCCAGCATAAGGCATTGGTGAACACCACCGGGTATCAAAATGACTCACCACTTCACGATGCAGCCAAGAATGGGCATGTGGATATAGTCAAGCTGTTACTTTCCTATGGAGCCTCCAGAAATGCTGTTAATATATTTGGTCTGCGGCCTGTCGATTATACAGATGATGAAAGTATGAAATCGCTATTGCTGCTACCAGAGAAGAATGAATCATCCTCAGCTAGCCACTGCTCAGTAATGAACACTGGGCAGCGTAGGGATGGACCTCTTGTACTTATAGGCAGTGGGCTGTCTTCAGAACAACAGAAAATGCTCAGTGAGCTTGCAGTAATTCTTAAGGCTAAAAAATATACTGAGTTTGACAGTACAGTAACTCATGTTGTTGTTCCTGGTGATGCAGTTCAAAGTACCTTGAAGTGTATGCTTGGGATTCTCAATGGATGCTGGATTCTAAAATTTGAATGGGTAAAAGCATGTCTACGAAGAAAAGTATGTGAACAGGAAGAAAAGTATGAAATTCCTGAAGGTCCACGCAGAAGCAGGCTCAACAGAGAACAGCTGTTGCCAAAGCTGTTTGATGGATGCTACTTCTATTTGTGGGGAACCTTCAAACACCATCCAAAGGACAACCTTATTAAGCTCGTCACTGCAGGTGGGGGCCAGATCCTCAGTAGAAAGCCCAAGCCAGACAGTGACGTGACTCAGACCATCAATACAGTCGCATACCATGCGAGACCCGATTCTGATCAGCGCTTCTGCACACAGTATATCATCTATGAAGATTTGTGTAATTATCACCCAGAGAGGGTTCGGCAGGGCAAAGTCTGGAAGGCTCCTTCGAGCTGGTTTATAGACTGTGTGATGTCCTTTGAGTTGCTTCCTCTTGACAGCTGAATATTATACCAGATGAACATTTCAAATTGAATTTGCACGGTTTGTGAGAGCCCAGTCATTGTACTGTTTTTAATGTTCACATTTTTACAAATAGGTAGAGTCATTCATATTTGTCTTTGAATCAAAAAAAAAAAAAAAAAA
  3.  
Jan 28 '11 #1
1 1566
numberwhun
3,509 Expert Mod 2GB
You may want to post this question over on the BioPerl forum. I don't know of anyone here who has experience with it, sorry.
Jan 28 '11 #2

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