Harvard:Biophysics 101/2007/03/15

From OpenWetWare

Revision as of 12:07, 14 March 2007

Assignment Due Mar 20

Exonic mutation finder

Below is a exonic sequence of a gene. Which gene is it? Is it mutated? Is the allele implicated in disease? Which diseases?

>Example_a_exon

       1 cttagcggta gccccttggt ttccgtggca acggaaaagc gcgggaatta cagataaatt
      61 aaaactgcga ctgcgcggcg tgagctcgct gagacttcct ggacggggga caggctgtgg
     121 ggtttctcag ataactgggc ccctgcgctc aggaggcctt caccctctgc tctgggtaaa
     181 gttcattgga acagaaagaa atggatttat ctgctcttcg cgttgaagaa gtacaaaatg
     241 tcattaatgc tatgcagaaa atcttagagt gtcccatctg tctggagttg atcaaggaac
     301 ctgtctccac aaagtgtgac cacatatttt gcaaattttg catgctgaaa cttctcaacc
     361 agaagaaagg gccttcacag tgtcctttat gtaagaatga tataaccaaa aggagcctac
     421 aagaaagtac gagatttagt caacttgttg aagagctatt gaaaatcatt tgtgcttttc
     481 agcttgacac aggtttggag tatgcaaaca gctataattt tgcaaaaaag gaaaataact
     541 ctcctgaaca tctaaaagat gaagtttcta tcatccaaag tatgggctac agaaaccgtg
     601 ccaaaagact tctacagagt gaacccgaaa atccttcctt gcaggaaacc agtctcagtg
     661 tccaactctc taaccttgga actgtgagaa ctctgaggac aaagcagcgg atacaacctc
     721 aaaagacgtc tgtctacatt gaattgggat ctgattcttc tgaagatacc gttaataagg
     781 caacttattg cagtgtggga gatcaagaat tgttacaaat cacccctcaa ggaaccaggg
     841 atgaaatcag tttggattct gcaaaaaagg ctgcttgtga attttctgag acggatgtaa
     901 caaatactga acatcatcaa cccagtaata atgatttgaa caccactgag aagcgtgcag
     961 ctgagaggca tccagaaaag tatcagggta gttctgtttc aaacttgcat gtggagccat
    1021 gtggcacaaa tactcatgcc agctcattac agcatgagaa cagcagttta ttactcacta
    1081 aagacagaat gaatgtagaa aaggctgaat tctgtaataa aagcaaacag cctggcttag
    1141 caaggagcca acataacaga tgggctggaa gtaaggaaac atgtaatgat aggcggactc
    1201 ccagcacaga aaaaaaggta gatctgaatg ctgatcccct gtgtgagaga aaagaatgga
    1261 ataagcagaa actgccatgc tcagagaatc ctagagatac tgaagatgtt ccttggataa
    1321 cactaaatag cagcattcag aaagttaatg agtggttttc cagaagtgat gaactgttag
    1381 gttctgatga ctcacatgat ggggagtctg aatcaaatgc caaagtagct gatgtattgg
    1441 acgttctaaa tgaggtagat gaatattctg gttcttcaga gaaaatagac ttactggcca
    1501 gtgatcctca tgaggcttta atatgtaaaa gtgaaagagt tcactccaaa tcagtagaga
    1561 gtaatattga agacaaaata tttgggaaaa cctatcggaa gaaggcaagc ctccccaact
    1621 taagccatgt aactgaaaat ctaattatag gagcatttgt tactgagcca cagataatac
    1681 aagagcgtcc cctcacaaat aaattaaagc gtaaaaggag acctacatca ggccttcatc
    1741 ctgaggattt tatcaagaaa gcagatttgg cagttcaaaa gactcctgaa atgataaatc
    1801 agggaactaa ccaaacggag cagaatggtc aagtgatgaa tattactaat agtggtcatg
    1861 agaataaaac aaaaggtgat tctattcaga atgagaaaaa tcctaaccca atagaatcac
    1921 tagaaaaaga atctgctttc aaaacgaaag ctgaacctat aagcagcagt ataagcaata
    1981 tggaactcga attaaatatc cacaattcaa aagcacctaa aaagaatagg ctgaggagga
    2041 agtcttctac caggcatatt catgcgcttg aactagtagt cagtagaaat ctaagcccac
    2101 ctaattgtac tgaattgcaa attgatagtt gttctagcag tgaagagata aagaaaaaaa
    2161 agtacaacca aatgccagtc aggcacagca gaaacctaca actcatggaa ggtaaagaac
    2221 ctgcaactgg agccaagaag agtaacaagc caaatgaaca gacaagtaaa agacatgaca
    2281 gcgatacttt cccagagctg aagttaacaa atgcacctgg ttcttttact aagtgttcaa
    2341 ataccagtga acttaaagaa tttgtcaatc ctagccttcc aagagaagaa aaagaagaga
    2401 aactagaaac agttaaagtg tctaataatg ctgaagaccc caaagatctc atgttaagtg
    2461 gagaaagggt tttgcaaact gaaagatctg tagagagtag cagtatttca ttggtacctg
    2521 gtactgatta tggcactcag gaaagtatct cgttactgga agttagcact ctagggaagg
    2581 caaaaacaga accaaataaa tgtgtgagtc agtgtgcagc atttgaaaac cccaagggac
    2641 taattcatgg ttgttccaaa gataatagaa atgacacaga aggctttaag tatccattgg
    2701 gacatgaagt taaccacagt cgggaaacaa gcatagaaat ggaagaaagt gaacttgatg
    2761 ctcagtattt gcagaataca ttcaaggttt caaagcgcca gtcatttgct ccgttttcaa
    2821 atccaggaaa tgcagaagag gaatgtgcaa cattctctgc ccactctggg tccttaaaga
    2881 aacaaagtcc aaaagtcact tttgaatgtg aacaaaagga agaaaatcaa ggaaagaatg
    2941 agtctaatat caagcctgta cagacagtta atatcactgc aggctttcct gtggttggtc
    3001 agaaagataa gccagttgat aatgccaaat gtagtatcaa aggaggctct aggttttgtc
    3061 tatcatctca gttcagaggc aacgaaactg gactcattac tccaaataaa catggacttt
    3121 tacaaaaccc atatcgtata ccaccacttt ttcccatcaa gtcatttgtt aaaactaaat
    3181 gtaagaaaaa tctgctagag gaaaactttg aggaacattc aatgtcacct gaaagagaaa
    3241 tgggaaatga gaacattcca agtacagtga gcacaattag ccgtaataac attagagaaa
    3301 atgtttttaa agaagccagc tcaagcaata ttaatgaagt aggttccagt actaatgaag
    3361 tgggctccag tattaatgaa ataggttcca gtgatgaaaa cattcaagca gaactaggta
    3421 gaaacagagg gccaaaattg aatgctatgc ttagattagg ggttttgcaa cctgaggtct
    3481 ataaacaaag tcttcctgga agtaattgta agcatcctga aataaaaaag caagaatatg
    3541 aagaagtagt tcagactgtt aatacagatt tctctccata tctgatttca gataacttag
    3601 aacagcctat gggaagtagt catgcatctc aggtttgttc tgagacacct gatgacctgt
    3661 tagatgatgg tgaaataaag gaagatacta gttttgctga aaatgacatt aaggaaagtt
    3721 ctgctgtttt tagcaaaagc gtccagaaag gagagcttag caggagtcct agccctttca
    3781 cccatacaca tttggctcag ggttaccgaa gaggggccaa gaaattagag tcctcagaag
    3841 agaacttatc tagtgaggat gaagagcttc cctgcttcca acacttgtta tttggtaaag
    3901 taaacaatat accttctcag tctactaggc atagcaccgt tgctaccgag tgtctgtcta
    3961 agaacacaga ggagaattta ttatcattga agaatagctt aaatgactgc agtaaccagg
    4021 taatattggc aaaggcatct caggaacatc accttagtga ggaaacaaaa tgttctgcta
    4081 gcttgttttc ttcacagtgc agtgaattgg aagacttgac tgcaaataca aacacccagg
    4141 atcctttctt gattggttct tccaaacaaa tgaggcatca gtctgaaagc cagggagttg
    4201 gtctgagtga caaggaattg gtttcagatg atgaagaaag aggaacgggc ttggaagaaa
    4261 ataatcaaga agagcaaagc atggattcaa acttaggtga agcagcatct gggtgtgaga
    4321 gtgaaacaag cgtctctgaa gactgctcag ggctatcctc tcagagtgac attttaacca
    4381 ctcagcagag ggataccatg caacataacc tgataaagct ccagcaggaa atggctgaac
    4441 tagaagctgt gttagaacag catgggagcc agccttctaa cagctaccct tccatcataa
    4501 gtgactcttc tgcccttgag gacctgcgaa atccagaaca aagcacatca gaaaaagcag
    4561 tattaacttc acagaaaagt agtgaatacc ctataagcca gaatccagaa ggcctttctg
    4621 ctgacaagtt tgaggtgtct gcagatagtt ctaccagtaa aaataaagaa ccaggagtgg
    4681 aaaggtcatc cccttctaaa tgcccatcat tagatgatag gtggtacatg cacagttgct
    4741 ctgggagtct tcagaataga aactacccat ctcaagagga gctcattaag gttgttgatg
    4801 tggaggagca acagctggaa gagtctgggc cacacgattt gacggaaaca tcttacttgc
    4861 caaggcaaga tctagaggga accccttacc tggaatctgg aatcagcctc ttctctgatg
    4921 accctgaatc tgatccttct gaagacagag ccccagagtc agctcgtgtt ggcaacatac
    4981 catcttcaac ctctgcattg aaagttcccc aattgaaagt tgcagaatct gcccagagtc
    5041 cagctgctgc tcatactact gatactgctg ggtataatgc aatggaagaa agtgtgagca
    5101 gggagaagcc agaattgaca gcttcaacag aaagggtcaa caaaagaatg tccatggtgg
    5161 tgtctggcct gaccccagaa gaatttatgc tcgtgtacaa gtttgccaga aaacaccaca
    5221 tcactttaac taatctaatt actgaagaga ctactcatgt tgttatgaaa acagatgctg
    5281 agtttgtgtg tgaacggaca ctgaaatatt ttctaggaat tgcgggagga aaatgggtag
    5341 ttagctattt ctgggtgacc cagtctatta aagaaagaaa aatgctgaat gagcatgatt
    5401 ttgaagtcag aggagatgtg gtcaatggaa gaaaccacca aggtccaaag cgagcaagag
    5461 aatcccagga cagaaagatc ttcagggggc tagaaatctg ttgctatggg cccttcacca
    5521 acatgcccac agatcaactg gaatggatgg tacagctgtg tggtgcttct gtggtgaagg
    5581 agctttcatc attcaccctt ggcacaggtg tccacccaat tgtggttgtg cagccagatg
    5641 cctggacaga ggacaatggc ttccatgcaa ttgggcagat gtgtgaggca cctgtggtga
    5701 cccgagagtg ggtgttggac agtgtagcac tctaccagtg ccaggagctg gacacctacc
    5761 tgatacccca gatcccccac agccactact gactgcagcc agccacaggt acagagccac
    5821 aggaccccaa gaatgagctt acaaagtggc ctttccaggc cctgggagct cctctcactc
    5881 ttcagtcctt ctactgtcct ggctactaaa tattttatgt acatcagcct gaaaaggact
    5941 tctggctatg caagggtccc ttaaagattt tctgcttgaa gtctcccttg gaaatctgcc
    6001 atgagcacaa aattatggta atttttcacc tgagaagatt ttaaaaccat ttaaacgcca
    6061 ccaattgagc aagatgctga ttcattattt atcagcccta ttctttctat tcaggctgtt
    6121 gttggcttag ggctggaagc acagagtggc ttggcctcaa gagaatagct ggtttcccta
    6181 agtttacttc tctaaaaccc tgtgttcaca aaggcagaga gtcagaccct tcaatggaag
    6241 gagagtgctt gggatcgatt atgtgactta aagtcagaat agtccttggg cagttctcaa
    6301 atgttggagt ggaacattgg ggaggaaatt ctgaggcagg tattagaaat gaaaaggaaa
    6361 cttgaaacct gggcatggtg gctcacgcct gtaatcccag cactttggga ggccaaggtg
    6421 ggcagatcac tggaggtcag gagttcgaaa ccagcctggc caacatggtg aaaccccatc
    6481 tctactaaaa atacagaaat tagccggtca tggtggtgga cacctgtaat cccagctact
    6541 caggtggcta aggcaggaga atcacttcag cccgggaggt ggaggttgca gtgagccaag
    6601 atcataccac ggcactccag cctgggtgac agtgagactg tggctcaaaa aaaaaaaaaa
    6661 aaaaaggaaa atgaaactag aagagatttc taaaagtctg agatatattt gctagatttc
    6721 taaagaatgt gttctaaaac agcagaagat tttcaagaac cggtttccaa agacagtctt
    6781 ctaattcctc attagtaata agtaaaatgt ttattgttgt agctctggta tataatccat
    6841 tcctcttaaa atataagacc tctggcatga atatttcata tctataaaat gacagatccc
    6901 accaggaagg aagctgttgc tttctttgag gtgatttttt tcctttgctc cctgttgctg
    6961 aaaccataca gcttcataaa taattttgct tgctgaagga agaaaaagtg tttttcataa
    7021 acccattatc caggactgtt tatagctgtt ggaaggacta ggtcttccct agccccccca
    7081 gtgtgcaagg gcagtgaaga cttgattgta caaaatacgt tttgtaaatg ttgtgctgtt
    7141 aacactgcaa ataaacttgg tagcaaacac ttcaaaaaaa aaaaaaaaaa a

• Write a script to automatically carry out the interpretation you performed manually.