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Accessing and Manipulating Biological Databases Solutions (Part-3)

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Below are the solutions to these Accessing and Manipulating Biological Data bases Part3

####################
#                  #
#    Exercise 1    #
#                  #
####################

library("seqinr")
seq1<-read.fasta(file="seq1.fasta")
sequences<-getSequence(seq1[[1]])
complementsequence<-comp(sequences,forceToLower = TRUE,ambiguous = FALSE)
print(complementsequence)

##    [1] "a" "g" "g" "a" "a" "a" "a" "g" "a" "a" "a" "a" "a" "t" "t" "t" "t"
##   [18] "t" "t" "t" "t" "t" "t" "g" "t" "g" "a" "c" "g" "t" "t" "g" "a" "c"
##   [35] "c" "t" "t" "g" "t" "c" "a" "a" "a" "g" "a" "c" "t" "a" "g" "a" "g"
##   [52] "t" "t" "t" "t" "c" "c" "g" "t" "t" "c" "g" "g" "a" "g" "a" "a" "g"
##   [69] "g" "g" "c" "a" "c" "a" "c" "t" "a" "g" "a" "a" "a" "t" "a" "t" "t"
##   [86] "a" "a" "a" "t" "g" "t" "g" "a" "g" "a" "a" "a" "a" "g" "g" "c" "a"
##  [103] "c" "t" "c" "g" "a" "a" "a" "g" "a" "a" "t" "g" "g" "a" "g" "g" "g"
##  [120] "a" "a" "a" "a" "a" "a" "a" "t" "a" "t" "t" "g" "a" "g" "a" "g" "g"
##  [137] "t" "a" "t" "a" "a" "g" "a" "g" "a" "t" "a" "a" "g" "t" "a" "t" "g"
##  [154] "t" "a" "t" "a" "t" "a" "g" "g" "t" "a" "a" "t" "a" "t" "a" "a" "t"
##  [171] "c" "a" "t" "c" "a" "c" "c" "t" "t" "a" "t" "t" "a" "a" "a" "a" "a"
##  [188] "t" "a" "a" "a" "a" "a" "t" "a" "a" "a" "t" "a" "a" "a" "a" "a" "a"
##  [205] "a" "a" "c" "c" "g" "a" "a" "a" "t" "c" "a" "t" "g" "a" "a" "c" "g"
##  [222] "t" "g" "g" "g" "a" "g" "t" "g" "t" "g" "t" "g" "t" "g" "a" "g" "a"
##  [239] "g" "g" "g" "c" "t" "c" "t" "t" "g" "g" "t" "c" "t" "t" "c" "a" "g"
##  [256] "c" "c" "a" "a" "c" "c" "c" "a" "c" "a" "a" "a" "t" "a" "t" "a" "t"
##  [273] "t" "a" "c" "t" "t" "c" "t" "t" "a" "a" "t" "a" "c" "c" "c" "c" "g"
##  [290] "a" "c" "a" "a" "a" "c" "t" "a" "g" "c" "t" "c" "c" "a" "c" "a" "a"
##  [307] "g" "t" "t" "t" "a" "c" "g" "a" "a" "a" "a" "t" "t" "g" "g" "t" "g"
##  [324] "g" "c" "a" "a" "c" "c" "a" "c" "g" "a" "a" "a" "g" "c" "g" "a" "c"
##  [341] "g" "g" "a" "a" "g" "t" "c" "g" "g" "a" "c" "t" "a" "c" "t" "g" "g"
##  [358] "t" "a" "t" "c" "g" "a" "c" "a" "c" "c" "c" "t" "t" "g" "g" "c" "t"
##  [375] "g" "a" "t" "a" "a" "c" "c" "g" "a" "g" "a" "t" "g" "a" "g" "g" "t"
##  [392] "c" "t" "c" "c" "c" "c" "a" "a" "a" "c" "g" "t" "t" "c" "t" "g" "g"
##  [409] "t" "t" "t" "t" "c" "a" "c" "a" "g" "t" "c" "a" "c" "t" "c" "t" "t"
##  [426] "a" "c" "t" "t" "t" "g" "g" "t" "c" "g" "t" "t" "t" "t" "t" "c" "t"
##  [443] "t" "g" "c" "t" "c" "c" "t" "t" "c" "a" "a" "t" "a" "c" "t" "g" "g"
##  [460] "g" "t" "a" "a" "g" "g" "c" "c" "t" "a" "a" "t" "a" "c" "c" "t" "c"
##  [477] "t" "t" "g" "g" "a" "c" "g" "a" "c" "g" "g" "a" "t" "c" "t" "t" "c"
##  [494] "c" "c" "t" "t" "a" "a" "a" "g" "t" "t" "t" "c" "c" "a" "g" "a" "c"
##  [511] "a" "c" "g" "t" "t" "c" "g" "t" "t" "t" "a" "a" "c" "t" "a" "g" "t"
##  [528] "g" "a" "a" "g" "g" "g" "t" "c" "t" "c" "c" "t" "a" "c" "g" "t" "c"
##  [545] "t" "a" "a" "t" "g" "c" "t" "t" "c" "g" "a" "c" "t" "g" "t" "g" "t"
##  [562] "c" "g" "t" "c" "t" "t" "a" "t" "a" "a" "a" "g" "g" "a" "g" "g" "c"
##  [579] "c" "c" "g" "g" "c" "a" "c" "t" "c" "c" "c" "g" "g" "a" "g" "g" "t"
##  [596] "c" "g" "t" "a" "a" "a" "a" "g" "g" "g" "t" "t" "a" "g" "g" "a" "c"
##  [613] "t" "c" "a" "c" "a" "c" "t" "a" "a" "g" "a" "c" "g" "a" "a" "a" "a"
##  [630] "g" "t" "a" "c" "c" "c" "a" "c" "c" "g" "g" "a" "g" "a" "c" "g" "t"
##  [647] "a" "g" "c" "g" "t" "c" "g" "g" "t" "c" "g" "c" "t" "c" "a" "a" "g"
##  [664] "a" "t" "g" "t" "t" "t" "t" "g" "a" "g" "c" "t" "g" "t" "g" "t" "t"
##  [681] "g" "t" "a" "g" "t" "a" "g" "g" "a" "c" "t" "c" "a" "c" "g" "g" "c"
##  [698] "c" "g" "t" "a" "g" "a" "a" "g" "a" "a" "g" "c" "a" "c" "a" "g" "a"
##  [715] "c" "g" "t" "c" "c" "a" "g" "a" "c" "t" "c" "a" "t" "t" "g" "t" "a"
##  [732] "g" "t" "a" "a" "c" "c" "g" "t" "a" "g" "t" "a" "t" "c" "a" "c" "a"
##  [749] "t" "g" "t" "a" "t" "a" "g" "a" "c" "g" "g" "t" "t" "a" "c" "g" "g"
##  [766] "c" "c" "t" "c" "t" "g" "g" "g" "g" "a" "g" "g" "t" "t" "c" "t" "c"
##  [783] "g" "c" "t" "g" "a" "g" "g" "t" "t" "t" "t" "t" "c" "t" "t" "a" "t"
##  [800] "c" "a" "a" "t" "g" "a" "g" "t" "a" "t" "g" "c" "c" "g" "a" "c" "c"
##  [817] "a" "g" "g" "a" "a" "g" "a" "t" "g" "a" "a" "g" "c" "c" "c" "c" "g"
##  [834] "g" "g" "a" "c" "a" "g" "g" "a" "a" "g" "t" "a" "g" "t" "a" "g" "c"
##  [851] "g" "g" "c" "t" "c" "t" "a" "c" "c" "a" "g" "c" "c" "c" "c" "a" "c"
##  [868] "g" "a" "c" "c" "g" "c" "c" "a" "c" "g" "t" "g" "t" "a" "c" "a" "a"
##  [885] "a" "t" "a" "g" "c" "t" "g" "g" "c" "c" "g" "t" "g" "t" "t" "t" "g"
##  [902] "t" "c" "g" "a" "c" "g" "c" "c" "c" "g" "g" "t" "g" "c" "c" "g" "g"
##  [919] "g" "c" "g" "c" "g" "g" "t" "g" "c" "c" "t" "g" "a" "t" "g" "g" "a"
##  [936] "g" "g" "t" "c" "c" "g" "g" "a" "g" "a" "c" "g" "g" "t" "a" "g" "t"
##  [953] "g" "g" "g" "c" "g" "t" "a" "g" "g" "g" "g" "t" "c" "g" "a" "t" "g"
##  [970] "g" "c" "g" "a" "t" "g" "g" "c" "g" "a" "t" "g" "g" "t" "c" "g" "c"
##  [987] "g" "g" "c" "g" "t" "c" "g" "g" "c" "g" "a" "g" "g" "t" "c" "g" "a"
## [1004] "g" "c" "g" "c" "g" "a" "g" "g" "t" "g" "c" "c" "t" "c" "g" "g" "g"
## [1021] "a" "g" "t" "g" "t" "g" "a" "g" "g" "t" "c" "c" "c" "t" "g" "c" "g"
## [1038] "g" "a" "g" "g" "g" "g" "g" "c" "a" "c" "c" "c" "g" "t" "a" "g" "t"
## [1055] "t" "c" "c" "c" "g" "a" "a" "g" "t" "t" "g" "t" "g" "g" "g" "a" "c"
## [1072] "g" "g" "c" "a" "g" "g" "t" "g" "c" "c" "t" "c" "t" "a" "g" "a" "g"
## [1089] "g" "t" "a" "c" "a" "t" "g" "t" "g" "c" "g" "a" "g" "t" "c" "g" "t"
## [1106] "c" "c" "c" "t" "g" "g" "g" "g" "g" "a" "c" "t" "t" "c" "c" "g" "g"
## [1123] "c" "g" "g" "t" "g" "g" "t" "g" "c" "g" "g" "g" "t" "g" "g" "c" "g"
## [1140] "g" "t" "g" "g" "a" "t" "g" "t" "t" "g" "a" "g" "g" "c" "t" "g" "t"
## [1157] "c" "c" "c" "t" "a" "t" "t" "g" "t" "c" "g" "a" "a" "g" "g" "a" "g"
## [1174] "g" "t" "c" "c" "a" "a" "g" "t" "g" "t" "t" "g" "a" "c" "a" "t" "a"
## [1191] "g" "g" "t" "c" "t" "t" "c" "c" "t" "c" "t" "t" "g" "t" "t" "c" "c"
## [1208] "t" "g" "a" "g" "a" "g" "a" "g" "g" "t" "g" "a" "g" "g" "t" "t" "g"
## [1225] "t" "g" "t" "c" "g" "g" "t" "t" "g" "g" "c" "g" "g" "c" "c" "t" "g"
## [1242] "g" "t" "g" "g" "g" "g" "g" "c" "a" "t" "a" "t" "t" "t" "c" "t" "g"
## [1259] "g" "c" "g" "c" "c" "c" "g" "g" "a" "g" "c" "g" "g" "t" "c" "t" "t"
## [1276] "c" "t" "g" "g" "c" "g" "c" "c" "c" "t" "c" "c" "t" "c" "c" "c" "g"
## [1293] "c" "g" "c" "c" "a" "g" "g" "g" "g" "c" "c" "c" "c" "c" "g" "c" "c"
## [1310] "c" "c" "g" "c" "c" "c" "c" "g" "c" "c" "c" "c" "t" "c" "t" "g" "g"
## [1327] "g" "t" "c" "t" "g" "g" "g" "a" "g" "g" "c" "g" "a" "c" "c" "c" "t"
## [1344] "c" "t" "g" "g" "a" "a" "g" "g" "t" "t" "t" "t" "c" "g" "t" "t" "t"
## [1361] "t" "t" "g" "t" "t" "t" "t" "t" "t" "g" "t" "t" "t" "t" "t" "t" "t"
## [1378] "t" "g" "t" "t" "t" "t" "t" "t" "t" "g" "t" "t" "t" "t" "t" "t" "g"
## [1395] "t" "t" "t" "t" "t" "t" "t" "g" "t" "g" "t" "g" "t" "g" "t" "g" "t"
## [1412] "g" "t" "t" "t" "t" "t" "t" "t" "c" "t" "c" "t" "t" "t" "t" "t" "t"
## [1429] "g" "t" "a" "t" "t" "g" "t" "t" "c" "a" "t" "t" "t" "a" "a" "a" "a"
## [1446] "t" "t" "t" "t" "t" "t" "t" "t" "c" "t" "t" "g" "t" "t" "t" "t" "a"
## [1463] "t" "a" "t" "t" "c" "t" "c" "c" "t" "t" "g" "t" "t" "t" "c" "t" "t"
## [1480] "c" "g" "t" "t" "t" "t" "g" "t" "t" "g" "t" "c" "c" "t" "t" "t" "a"
## [1497] "c" "a" "c" "c" "c" "t" "t" "t" "t" "a" "t" "a" "t" "t" "t" "g" "c"
## [1514] "t" "c" "c" "c" "t" "t" "c" "t" "t" "t" "t" "g" "t" "t" "t" "g" "a"
## [1531] "a" "a" "t" "t" "t" "t" "t" "t" "t" "t" "c" "g" "c" "t" "c" "t" "c"
## [1548] "c" "c" "t" "a" "t" "t" "t" "t" "t" "t" "a" "a" "t" "t" "t" "t" "t"
## [1565] "a" "t" "c" "t" "t" "t" "t" "a" "t" "t" "t" "a" "g" "a" "t" "t" "t"
## [1582] "t" "c" "t" "t" "t" "t" "a" "c" "g" "t" "a" "c" "t" "a" "a" "a" "g"
## [1599] "g" "g" "t" "a" "c" "a" "t" "g" "g" "t" "a" "a" "t" "a" "a" "a" "a"
## [1616] "t" "t" "g" "t" "a" "a" "a" "t" "t" "a" "t" "t" "t" "t" "t" "a" "g"
## [1633] "t" "t" "a" "a" "a" "t" "t" "t" "a" "c" "t" "t" "t" "t" "t" "t" "a"
## [1650] "t" "t" "t" "t" "c" "c" "c" "t" "t" "g" "g" "t" "t" "c" "t" "a" "t"
## [1667] "t" "g" "t" "a" "a" "t" "t" "t" "c" "g" "t" "t" "t" "t" "t" "t" "t"
## [1684] "t" "t" "t" "t" "t" "t" "t" "a" "c" "t" "c" "t" "t" "g" "t" "c" "t"
## [1701] "t" "t" "c" "c" "t" "t" "t" "c" "c" "c" "c" "t" "a" "c" "a" "g" "g"
## [1718] "a" "a" "a" "c" "a" "t" "a" "a" "a" "a" "a" "g" "t" "c" "c" "c" "a"
## [1735] "a" "a" "t" "a" "c" "a" "a" "t" "g" "a" "a" "a" "a" "a" "a" "a" "a"
## [1752] "a" "a" "a" "a" "a" "a" "a" "a" "a" "t" "t" "g" "a" "g" "c" "c" "c"
## [1769] "c" "t" "c" "t" "c" "a" "a" "t" "g" "a" "a" "a" "a" "g" "a" "c" "a"
## [1786] "a" "g" "g" "g" "a" "a" "a" "t" "t" "g" "g" "g" "g" "g" "t" "c" "g"
## [1803] "c" "c" "c" "g" "g" "g" "a" "c" "g" "g" "a" "g" "g" "g" "a" "c" "c"
## [1820] "c" "t" "c" "t" "a" "a" "c" "c" "c" "c" "c" "c" "g" "c" "t" "c" "t"
## [1837] "g" "a" "g" "t" "c" "c" "c" "c" "g" "g" "g" "a" "c" "c" "c" "c" "g"
## [1854] "g" "t" "c" "c" "a" "c" "t" "c" "g" "g" "a" "c" "g" "t" "c" "a" "g"
## [1871] "t" "g" "a" "c" "g" "g" "t" "c" "c" "a" "g" "g" "g" "a" "c" "c" "t"
## [1888] "c" "g" "g" "g" "g" "a" "c" "c" "c" "a" "c" "c" "c" "a" "c" "g" "g"
## [1905] "g" "g" "t" "c" "c" "t" "t" "g" "a" "g" "g" "t" "c" "c" "t" "t" "c"
## [1922] "c" "g" "a" "g" "t" "c" "t" "c" "g" "a" "g" "c" "t" "c" "g" "g" "c"
## [1939] "c" "g" "a" "g" "g" "c" "g" "g" "g" "t" "c" "g" "t" "a" "a" "c" "t"
## [1956] "a" "c" "c" "c" "c" "g" "t" "t" "a" "g" "c" "a" "t" "c" "c" "g" "g"
## [1973] "a" "g" "g" "t" "c" "c" "a" "c" "t" "g" "g" "c" "t" "c" "g" "g" "g"
## [1990] "a" "a" "c" "a" "g" "g" "g" "a" "g" "g" "a" "g" "a" "g" "g" "c" "a"
## [2007] "a" "t" "c" "c" "c" "a" "c" "g" "g" "a" "c" "c" "t" "c" "c" "c" "c"
## [2024] "c" "c" "a" "t" "g" "t" "g" "a" "a" "c" "c" "c" "c" "g" "a" "a" "c"
## [2041] "g" "g" "a" "c" "c" "g" "g" "g" "g" "t" "c" "c" "a" "a" "g" "g" "g"
## [2058] "t" "c" "a" "g" "g" "a" "a" "t" "t" "a" "c" "g" "a" "g" "g" "a" "a"
## [2075] "t" "t" "g" "g" "g" "t" "g" "a" "c" "a" "c" "t" "a" "c" "t" "g" "a"
## [2092] "a" "g" "g" "a" "t" "c" "c" "g" "g" "a" "a" "c" "t" "c" "c" "t" "t"
## [2109] "t" "c" "c" "c" "t" "t" "c" "c" "t" "c" "t" "c" "c" "c" "c" "t" "c"
## [2126] "c" "g" "a" "c" "g" "g" "c" "c" "a" "c" "c" "g" "a" "a" "t" "g" "g"
## [2143] "t" "t" "c" "t" "a" "c" "g" "g" "c" "c" "t" "t" "t" "g" "g" "g" "g"
## [2160] "c" "c" "t" "t" "a" "g" "g" "a" "g" "t" "c" "c" "c" "a" "c" "t" "c"
## [2177] "g" "g" "a" "g" "a" "a" "c" "c" "c" "c" "a" "g" "t" "a" "c" "a" "g"
## [2194] "g" "g" "g" "t" "t" "c" "g" "a" "g" "g" "a" "c" "a" "g" "g" "a" "a"
## [2211] "c" "c" "c" "c" "a" "g" "t" "c" "c" "t" "c" "t" "a" "c" "g" "g" "t"
## [2228] "g" "g" "g" "g" "g" "g" "g" "g" "g" "g" "g" "c" "c" "c" "c" "c" "t"
## [2245] "g" "t" "a" "c" "t" "t" "t" "g" "t" "c" "g" "a" "g" "a" "g" "g" "g"
## [2262] "a" "g" "g" "a" "g" "t" "g" "g" "g" "g" "a" "g" "t" "g" "g" "a" "g"
## [2279] "t" "c" "c" "c" "g" "g" "t" "g" "g" "a" "c" "t" "a" "c" "t" "g" "g"
## [2296] "g" "a" "c" "c" "c" "c" "g" "c" "t" "a" "c" "c" "a" "c" "c" "t" "g"
## [2313] "g" "g" "g" "g" "a" "c" "t" "g" "a" "g" "t" "a" "t" "t" "c" "g" "g"
## [2330] "g" "g" "g" "g" "t" "c" "a" "g" "g" "g" "g" "a" "c" "c" "c" "t" "t"
## [2347] "c" "c" "c" "c" "c" "a" "a" "g" "t" "a" "a" "c" "t" "g" "g" "g" "a"
## [2364] "a" "a" "c" "c" "c" "c" "c" "a" "g" "g" "a" "a" "c" "c" "t" "g" "a"
## [2381] "g" "t" "g" "a" "c" "t" "a" "c" "g" "g" "g" "g" "g" "a" "a" "c" "c"
## [2398] "c" "c" "g" "g" "g" "t" "c" "g" "c" "c" "c" "a" "a" "g" "t" "t" "g"
## [2415] "t" "t" "a" "c" "t" "g" "t" "g" "a" "c" "g" "t" "t" "t" "t" "t" "c"
## [2432] "c" "g" "a" "a" "g" "a" "a" "a" "a" "a" "t" "g" "t" "t" "t" "t" "c"
## [2449] "t" "t" "t" "t" "t" "c" "c" "t" "t" "t" "t" "t" "g" "t" "t" "c" "a"
## [2466] "c" "c" "a" "c" "t" "a" "a" "a" "a" "a" "a" "a" "a" "a" "t" "t" "a"
## [2483] "t" "t" "t" "t" "t" "t" "t" "g" "g" "t" "g" "t" "c" "t" "g" "a" "t"
## [2500] "a" "t" "t" "t" "a" "t" "t" "t" "a" "c" "a" "t" "t" "t" "a" "t" "g"
## [2517] "t" "t" "t" "t" "a" "t" "t" "c" "a" "c" "c" "t" "a" "a" "a" "t" "g"
## [2534] "a" "a" "c" "g" "t" "t" "c" "t" "t" "t" "t" "a" "g" "t" "c" "t" "a"
## [2551] "t" "c" "a" "t" "a" "a" "a" "a" "a" "g" "a" "a" "a" "a" "t" "t" "a"
## [2568] "a" "g" "a" "a" "a" "a" "g" "g" "t" "c" "g" "a" "a" "a" "t" "t" "t"
## [2585] "g" "a" "c" "a" "c" "t" "t" "t" "t" "g" "t" "t" "t" "t" "t" "t" "a"
## [2602] "c" "c" "c" "c" "g" "c" "c" "c" "c" "a" "c" "c" "c" "c" "c" "t" "g"
## [2619] "a" "a" "t" "t" "t" "g" "a" "a" "a" "t" "c" "g" "t" "c" "c" "c" "t"
## [2636] "t" "g" "a" "a" "c" "a" "t" "t" "t" "c" "t" "t" "t" "t" "t" "t" "t"
## [2653] "t" "t" "t" "g" "t" "c" "t" "t" "t" "t" "g" "c" "t" "t" "a" "t" "a"
## [2670] "t" "g" "t" "t" "t" "a" "g" "g" "t" "a" "a" "a" "t" "g" "t" "t" "t"
## [2687] "t" "t" "g" "t" "t" "t" "c" "g" "t" "t" "t" "t" "g" "g" "c" "a" "a"
## [2704] "c" "a" "c" "t" "c" "t" "c" "c" "a" "c" "t" "c" "t" "c" "g" "a" "c"
## [2721] "c" "c" "g" "a" "a" "c" "t" "t" "c" "c" "a" "a" "c" "c" "t" "c" "c"
## [2738] "c" "t" "c" "a" "t" "c" "g" "c" "c" "t" "t" "c" "c" "a" "g" "g" "g"
## [2755] "t" "c" "a" "c" "t" "c" "g" "a" "c" "g" "t" "c" "c" "c" "c" "c" "a"
## [2772] "g" "a" "g" "a" "c" "a" "c" "t" "a" "c" "c" "t" "t" "t" "c" "c" "a"
## [2789] "c" "c" "g" "a" "a" "g" "g" "a" "g" "t" "c" "t" "g" "t" "t" "c" "c"
## [2806] "t" "t" "c" "c" "a" "c" "g" "a" "c" "g" "c" "t" "t" "a" "c" "c" "c"
## [2823] "c" "c" "t" "t" "c" "t" "g" "t" "c" "t" "t" "a" "g" "g" "t" "t" "g"
## [2840] "t" "t" "t" "c" "t" "t" "t" "c" "t" "c" "t" "g" "g" "t" "g" "t" "g"
## [2857] "t" "g" "g" "g" "g" "t" "g" "t" "g" "c" "g" "t" "g" "t" "g" "t" "c"
## [2874] "c" "g" "t" "g" "c" "a" "a" "g" "t" "g" "t" "g" "t" "g" "t" "g" "t"
## [2891] "a" "t" "g" "t" "g" "t" "c" "a" "g" "g" "t" "g" "a" "a" "t" "c" "g"
## [2908] "g" "g" "t" "c" "g" "t" "g" "a" "c" "g" "t" "c" "a" "g" "t" "g" "a"
## [2925] "g" "t" "g" "t" "c" "c" "c" "t" "g" "t" "g" "t" "g" "a" "g" "t" "c"
## [2942] "a" "g" "a" "g" "t" "t" "g" "g" "g" "a" "a" "g" "g" "t" "a" "g" "g"
## [2959] "g" "t" "a" "t" "g" "t" "g" "c" "c" "g" "g" "t" "c" "c" "c" "c" "g"
## [2976] "c" "a" "c" "c" "g" "a" "g" "t" "t" "t" "c" "c" "t" "t" "t" "a" "a"
## [2993] "c" "t" "g" "a" "g" "t" "a" "c" "g" "g" "g" "a" "g" "g" "t" "t" "t"
## [3010] "c" "g" "g" "t" "a" "c" "c" "t" "g" "c" "t" "g" "t" "t" "g" "t" "t"
## [3027] "g" "a" "g" "g" "t" "g" "t" "g" "a" "c" "c" "g" "g" "a" "a" "a" "c"
## [3044] "a" "c" "a" "a" "g" "t" "a" "a" "g" "t" "g" "t" "t" "g" "g" "a" "g"
## [3061] "g" "g" "t" "t" "g" "t" "c" "t" "c" "g" "t" "a" "t" "g" "t" "g" "t"
## [3078] "a" "c" "t" "t" "g" "t" "g" "t" "g" "t" "g" "t" "a" "c" "g" "t" "g"
## [3095] "t" "g" "t" "a" "t" "g" "g" "g" "t" "g" "t" "g" "t" "g" "c" "g" "t"
## [3112] "g" "t" "g" "t" "a" "t" "g" "g" "g" "t" "g" "t" "g" "t" "g" "t" "g"
## [3129] "t" "g" "t" "g" "t" "g" "t" "g" "g" "t" "g" "a" "g" "c" "g" "t" "a"
## [3146] "c" "g" "t" "a" "c" "c" "c" "t" "t" "c" "c" "c" "g" "t" "g" "g" "g"
## [3163] "c" "a" "g" "a" "t" "c" "t" "t" "a" "g" "g" "t" "c" "c" "t" "g" "a"
## [3180] "c" "c" "t" "a" "a" "g" "g" "c" "c" "t" "t" "a" "a" "g" "g" "a" "a"
## [3197] "c" "g" "a" "c" "g" "t" "a" "c" "c" "g" "g" "a" "g" "a" "g" "a" "c"
## [3214] "c" "c" "g" "g" "a" "a" "t" "t" "a" "a" "a" "a" "g" "g" "g" "g" "g"
## [3231] "g" "t" "a" "c" "a" "t" "t" "c" "g" "t" "a" "c" "a" "c" "c" "t" "a"
## [3248] "a" "c" "t" "g" "g" "g" "t" "c" "t" "c" "t" "t" "c" "g" "t" "g" "a"
## [3265] "t" "t" "t" "c" "c" "g" "g" "g" "t" "a" "a" "g" "a" "a" "c" "g" "a"
## [3282] "g" "a" "t" "a" "c" "a" "t" "a" "g" "a" "c" "a" "c" "t" "g" "a" "a"
## [3299] "t" "t" "c" "t" "a" "g" "a" "c" "g" "g" "t" "g" "g" "a" "c" "g" "g"
## [3316] "g" "g" "c" "t" "c" "c" "t" "a" "t" "a" "c" "g" "g" "t" "c" "c" "c"
## [3333] "t" "a" "c" "t" "g" "g" "t" "c" "c" "t" "g" "t" "c" "g" "a" "c" "g"
## [3350] "g" "t" "g" "g" "t" "t" "c" "g" "g" "g" "g" "g" "t" "c" "c" "g" "a"
## [3367] "g" "t" "a" "g" "t" "a" "g" "t" "c" "a" "g" "t" "c" "g" "g" "a" "g"
## [3384] "a" "g" "t" "c" "t" "g" "t" "g" "t" "g" "t" "g" "t" "g" "t" "g" "t"
## [3401] "g" "t" "g" "t" "g" "t" "g" "g" "t" "a" "t" "a" "t" "g" "g" "a" "g"
## [3418] "g" "a" "g" "t" "g" "a" "c" "a" "c" "g" "a" "g" "g" "g" "g" "c" "t"
## [3435] "t" "g" "t" "g" "g" "a" "c" "g" "g" "g" "g" "g" "t" "g" "t" "a" "g"
## [3452] "g" "t" "t" "a" "c" "a" "g" "t" "t" "t" "c" "g" "t" "t" "t" "t" "t"
## [3469] "a" "t" "g" "t" "g" "t" "g" "t" "a" "c" "a" "c" "t" "c" "g" "t" "t"
## [3486] "t" "g" "t" "a" "t" "t" "t" "c" "g" "a" "c" "a" "a" "g" "t" "c" "c"
## [3503] "g" "t" "t" "t" "c" "t" "c" "c" "c" "c" "t" "t" "t" "c" "t" "g" "c"
## [3520] "g" "t" "c" "c" "c" "c" "a" "g" "g" "g" "g" "t" "t" "t" "c" "g" "g"
## [3537] "g" "a" "a" "g" "a" "a" "g" "t" "g" "a" "a" "a" "c" "a" "c" "a" "g"
## [3554] "g" "g" "g" "a" "a" "c" "g" "a" "c" "g" "c" "t" "a" "g" "t" "a" "c"
## [3571] "c" "t" "c" "t" "c" "a" "a" "t" "t" "t" "c" "t" "c" "c" "g" "a" "a"
## [3588] "g" "g" "a" "a" "c" "c" "c" "t" "c" "t" "t" "c" "t" "c" "g" "a" "g"
## [3605] "a" "c" "g" "g" "t" "g" "g" "t" "c" "c" "c" "g" "a" "a" "g" "g" "g"
## [3622] "g" "t" "c" "a" "c" "a" "g" "a" "a" "a" "c" "c" "c" "c" "c" "a" "g"
## [3639] "a" "c" "a" "c" "t" "t" "t" "t" "t" "c" "t" "c" "c" "t" "a" "g" "g"
## [3656] "a" "g" "a" "c" "t" "c" "c" "a" "a" "a" "t" "g" "a" "c" "c" "c" "t"
## [3673] "c" "c" "c" "g" "a" "g" "t" "t" "c" "c" "g" "a" "c" "t" "c" "c" "c"
## [3690] "t" "t" "a" "c" "c" "t" "c" "t" "c" "c" "t" "t" "t" "t" "a" "a" "a"
## [3707] "a" "t" "c" "g" "t" "c" "a" "a" "g" "g" "t" "a" "g" "g" "g" "t" "c"
## [3724] "a" "c" "a" "t" "t" "c" "c" "t" "g" "g" "t" "t" "g" "g" "g" "g" "t"
## [3741] "t" "t" "t" "c" "a" "a" "t" "t" "t" "g" "a" "a" "c" "g" "t" "g" "g"
## [3758] "t" "g" "t" "c" "t" "g" "a" "t" "t" "t" "c" "c" "a" "g" "t" "t" "c"
## [3775] "c" "c" "g" "t" "a" "g" "g" "a" "c" "a" "c" "a" "a" "a" "g" "a" "g"
## [3792] "g" "g" "g" "a" "a" "a" "g" "a" "a" "g" "g" "g" "g" "t" "c" "t" "c"
## [3809] "a" "c" "t" "g" "t" "t" "c" "c" "c" "g" "g" "t" "c" "a" "a" "g" "t"
## [3826] "c" "t" "g" "a" "c" "t" "g" "t" "c" "t" "t" "t" "a" "g" "g" "t" "t"
## [3843] "g" "t" "c" "g" "a" "a" "a" "g" "g" "a" "c" "t" "c" "g" "a" "c" "c"
## [3860] "t" "t" "t" "a" "a" "a" "g" "t" "c" "t" "t" "g" "t" "c" "a" "g" "a"
## [3877] "c" "g" "t" "t" "c" "a" "a" "t" "g" "a" "g" "g" "g" "t" "c" "c" "a"
## [3894] "c" "t" "g" "a" "c" "t" "t" "c" "c" "a" "g" "t" "t" "c" "c" "a" "c"
## [3911] "t" "c" "c" "g" "g" "g" "g" "g" "g" "a" "c" "g" "g" "a" "g" "a" "c"
## [3928] "g" "g" "a" "c" "g" "c" "t" "c" "a" "g" "a" "g" "g" "g" "g" "g" "c"
## [3945] "c" "a" "a" "a" "c" "g" "t" "a" "a" "a" "a" "a" "g" "a" "a" "c" "t"
## [3962] "g" "t" "g" "g" "c" "c" "g" "t" "a" "a" "a" "g" "g" "a" "c" "t" "c"
## [3979] "c" "a" "a" "c" "t" "c" "g" "a" "g" "a" "g" "a" "c" "c" "c" "c" "t"
## [3996] "c" "a" "a" "g" "a" "t" "c" "t" "c" "t" "t" "a" "c" "c" "g" "a" "t"
## [4013] "c" "a" "t" "t" "c" "c" "g" "a" "a" "a" "a" "a" "c" "t" "c" "g" "a"
## [4030] "a" "c" "g" "t" "g" "t" "a" "g" "a" "g" "t" "g" "g" "a" "c" "g" "g"
## [4047] "a" "a" "a" "g" "g" "a" "c" "a" "g" "a" "a" "a" "a" "c" "g" "g" "a"
## [4064] "c" "c" "c" "t" "t" "t" "c" "c" "t" "t" "t" "c" "a" "a" "t" "a" "a"
## [4081] "a" "a" "g" "g" "g" "t" "c" "c" "a" "g" "t" "c" "g" "t" "t" "c" "c"
## [4098] "c" "c" "g" "t" "c" "t" "t" "g" "t" "a" "g" "c" "c" "g" "g" "t" "c"
## [4115] "g" "g" "g" "t" "c" "g" "g" "g" "t" "c" "t" "t" "c" "a" "t" "g" "t"
## [4132] "c" "c" "c" "c" "c" "t" "c" "c" "a" "g" "t" "a" "c" "c" "c" "g" "g"
## [4149] "g" "a" "c" "c" "c" "c" "g" "t" "c" "t" "t" "g" "t" "t" "a" "c" "c"
## [4166] "c" "t" "c" "t" "g" "t" "t" "a" "a" "g" "t" "t" "c" "c" "a" "c" "a"
## [4183] "c" "c" "a" "t" "t" "g" "t" "t" "g" "t" "t" "g" "g" "t" "t" "c" "a"
## [4200] "a" "c" "g" "g" "g" "a" "g" "t" "c" "a" "g" "a" "c" "c" "c" "g" "t"
## [4217] "c" "t" "t" "t" "g" "a" "c" "t" "t" "g" "a" "g" "a" "t" "g" "g" "g"
## [4234] "g" "a" "g" "a" "g" "g" "g" "t" "g" "g" "g" "g" "t" "t" "a" "g" "a"
## [4251] "a" "c" "g" "g" "g" "c" "g" "g" "t" "a" "g" "g" "g" "t" "g" "g" "t"
## [4268] "c" "t" "a" "a" "g" "g" "t" "c" "t" "g" "g" "a" "t" "t" "t" "c" "c"
## [4285] "c" "t" "a" "g" "t" "t" "c" "c" "t" "a" "c" "t" "c" "t" "c" "g" "c"
## [4302] "t" "t" "c" "c" "c" "t" "c" "t" "t" "c" "c" "c" "t" "c" "c" "c" "a"
## [4319] "g" "g" "g" "g" "t" "t" "c" "t" "t" "t" "t" "g" "g" "c" "g" "t" "g"
## [4336] "g" "g" "t" "t" "c" "g" "c" "t" "c" "g" "t" "g" "a" "c" "a" "g" "a"
## [4353] "c" "t" "t" "c" "t" "c" "t" "t" "t" "t" "t" "g" "a" "t" "c" "g" "a"
## [4370] "g" "g" "t" "c" "a" "a" "g" "a" "g" "g" "c" "t" "t" "a" "a" "g" "a"
## [4387] "c" "c" "g" "t" "c" "t" "c" "g" "c" "a" "g" "a" "c" "c" "c" "t" "t"
## [4404] "c" "c" "g" "c" "t" "a" "g" "t" "c" "a" "c" "g" "a" "a" "g" "a" "a"
## [4421] "a" "g" "g" "t" "a" "c" "c" "g" "c" "g" "t" "t" "c" "c" "g" "g" "a"
## [4438] "c" "c" "c" "a" "a" "g" "a" "c" "c" "c" "a" "c" "a" "c" "g" "a" "a"
## [4455] "c" "t" "t" "c" "t" "t" "t" "c" "g" "g" "t" "g" "a" "c" "c" "c" "c"
## [4472] "a" "c" "a" "c" "c" "c" "c" "a" "c" "t" "g" "t" "a" "g" "c" "g" "g"
## [4489] "t" "a" "c" "c" "g" "a" "c" "t" "c" "t" "t" "c" "c" "c" "c" "g" "a"
## [4506] "t" "c" "c" "c" "c" "c" "a" "g" "g" "c" "c" "t" "c" "c" "c" "t" "t"
## [4523] "c" "c" "t" "c" "g" "g" "t" "c" "c" "t" "g" "g" "c" "c" "t" "t" "g"
## [4540] "a" "c" "g" "t" "t" "c" "c" "c" "g" "c" "a" "a" "c" "g" "a" "c" "g"
## [4557] "g" "g" "t" "c" "c" "c" "c" "a" "c" "a" "c" "c" "t" "a" "c" "t" "a"
## [4574] "a" "c" "g" "a" "g" "t" "a" "c" "a" "g" "g" "t" "c" "g" "a" "g" "t"
## [4591] "c" "t" "g" "g" "t" "c" "a" "a" "g" "t" "t" "c" "t" "t" "t" "g" "a"
## [4608] "t" "t" "g" "g" "a" "g" "g" "t" "a" "a" "a" "t" "a" "a" "a" "a" "g"
## [4625] "a" "a" "c" "c" "a" "c" "t" "c" "a" "g" "g" "a" "a" "a" "a" "a" "a"
## [4642] "a" "a" "a" "a" "a" "a" "a" "g" "t" "c" "t" "g" "a" "c" "a" "a" "t"
## [4659] "t" "g" "t" "c" "t" "t" "t" "t" "t" "t" "t" "t" "a" "a" "a" "a" "t"
## [4676] "t" "t" "t" "t" "c" "g" "t" "c" "t" "t" "t" "t" "g" "a" "c" "t" "t"
## [4693] "t" "t" "t" "t" "t" "t" "t" "t" "a" "g" "g" "a" "c" "c" "a" "t" "g"
## [4710] "t" "a" "c" "t" "t" "t" "a" "t" "t" "t" "c" "t" "a" "a" "a" "a" "a"
## [4727] "a" "a" "a" "a" "a" "a" "a" "t" "a" "t"

####################
#                  #
#    Exercise 2    #
#                  #
####################

library("seqinr")
c <- tablecode()

print(c)

## NULL

####################
#                  #
#    Exercise 3    #
#                  #
####################

library("seqinr")
c <- tablecode(2)

print(c)

## NULL

####################
#                  #
#    Exercise 4    #
#                  #
####################

library("seqinr")
c<-syncodons('aaa',numcode = 1)
print(c)

## $aaa
## [1] "aaa" "aag"

####################
#                  #
#    Exercise 5    #
#                  #
####################

library("seqinr")
seq1<-read.fasta(file="seq1.fasta")
sequences<-getSequence(seq1[[1]])
Amino<-getTrans(sequences, sens = "F", numcode = 2,NAstring = "X", ambiguous = FALSE)
print(aaa(Amino))

##    [1] "Ser" "Phe" "Ser" "Phe" "Stp" "Lys" "Lys" "Asn" "Thr" "Ala" "Thr"
##   [12] "Gly" "Thr" "Val" "Ser" "Asp" "Leu" "Lys" "Stp" "Gln" "Ala" "Ser"
##   [23] "Ser" "Arg" "Val" "Ile" "Phe" "Met" "Ile" "Tyr" "Thr" "Leu" "Phe"
##   [34] "Arg" "Glu" "Leu" "Ser" "Tyr" "Leu" "Pro" "Phe" "Phe" "Met" "Thr"
##   [45] "Leu" "His" "Ile" "Leu" "Tyr" "Ser" "Tyr" "Met" "Tyr" "Pro" "Leu"
##   [56] "Tyr" "Stp" "Stp" "Trp" "Asn" "Asn" "Phe" "Tyr" "Phe" "Tyr" "Leu"
##   [67] "Phe" "Phe" "Leu" "Ala" "Leu" "Val" "Leu" "Ala" "Pro" "Ser" "His"
##   [78] "Thr" "Leu" "Ser" "Arg" "Glu" "Pro" "Glu" "Val" "Gly" "Trp" "Val"
##   [89] "Phe" "Met" "Stp" "Trp" "Stp" "Ile" "Met" "Gly" "Leu" "Phe" "Asp"
##  [100] "Arg" "Gly" "Val" "Gln" "Met" "Leu" "Leu" "Thr" "Thr" "Val" "Gly"
##  [111] "Ala" "Phe" "Ala" "Ala" "Phe" "Ser" "Leu" "Met" "Thr" "Met" "Ala"
##  [122] "Val" "Gly" "Thr" "Asp" "Tyr" "Trp" "Leu" "Tyr" "Ser" "Stp" "Gly"
##  [133] "Val" "Cys" "Lys" "Thr" "Lys" "Ser" "Val" "Ser" "Glu" "Asn" "Glu"
##  [144] "Thr" "Ser" "Lys" "Lys" "Asn" "Glu" "Glu" "Val" "Met" "Thr" "His"
##  [155] "Ser" "Gly" "Leu" "Trp" "Stp" "Thr" "Cys" "Cys" "Leu" "Glu" "Gly"
##  [166] "Asn" "Phe" "Lys" "Gly" "Leu" "Cys" "Lys" "Gln" "Ile" "Asp" "His"
##  [177] "Phe" "Pro" "Glu" "Asp" "Ala" "Asp" "Tyr" "Glu" "Ala" "Asp" "Thr"
##  [188] "Ala" "Glu" "Tyr" "Phe" "Leu" "Arg" "Ala" "Val" "Stp" "Ala" "Ser"
##  [199] "Ser" "Ile" "Phe" "Pro" "Ile" "Leu" "Ser" "Val" "Ile" "Leu" "Leu"
##  [210] "Phe" "Met" "Gly" "Gly" "Leu" "Cys" "Ile" "Ala" "Ala" "Ser" "Glu"
##  [221] "Phe" "Tyr" "Lys" "Thr" "Arg" "His" "Asn" "Ile" "Ile" "Leu" "Ser"
##  [232] "Ala" "Gly" "Ile" "Phe" "Phe" "Val" "Ser" "Ala" "Gly" "Leu" "Ser"
##  [243] "Asn" "Ile" "Ile" "Gly" "Ile" "Met" "Val" "Tyr" "Met" "Ser" "Ala"
##  [254] "Asn" "Ala" "Gly" "Asp" "Pro" "Ser" "Lys" "Ser" "Asp" "Ser" "Lys"
##  [265] "Lys" "Asn" "Ser" "Tyr" "Ser" "Tyr" "Gly" "Trp" "Ser" "Phe" "Tyr"
##  [276] "Phe" "Gly" "Ala" "Leu" "Ser" "Phe" "Ile" "Ile" "Ala" "Glu" "Met"
##  [287] "Val" "Gly" "Val" "Leu" "Ala" "Val" "His" "Met" "Phe" "Ile" "Asp"
##  [298] "Arg" "His" "Lys" "Gln" "Leu" "Arg" "Ala" "Thr" "Ala" "Arg" "Ala"
##  [309] "Thr" "Asp" "Tyr" "Leu" "Gln" "Ala" "Ser" "Ala" "Ile" "Thr" "Arg"
##  [320] "Ile" "Pro" "Ser" "Tyr" "Arg" "Tyr" "Arg" "Tyr" "Gln" "Arg" "Arg"
##  [331] "Ser" "Arg" "Ser" "Ser" "Ser" "Arg" "Ser" "Thr" "Glu" "Pro" "Ser"
##  [342] "His" "Ser" "Stp" "Asp" "Ala" "Ser" "Pro" "Val" "Gly" "Ile" "Lys"
##  [353] "Gly" "Phe" "Asn" "Thr" "Leu" "Pro" "Ser" "Thr" "Glu" "Ile" "Ser"
##  [364] "Met" "Tyr" "Thr" "Leu" "Ser" "Stp" "Asp" "Pro" "Leu" "Lys" "Ala"
##  [375] "Ala" "Thr" "Thr" "Pro" "Thr" "Ala" "Thr" "Tyr" "Asn" "Ser" "Asp"
##  [386] "Stp" "Asp" "Asn" "Ser" "Phe" "Leu" "Gln" "Val" "His" "Asn" "Cys"
##  [397] "Ile" "Gln" "Lys" "Glu" "Asn" "Lys" "Asp" "Ser" "Leu" "His" "Ser"
##  [408] "Asn" "Thr" "Ala" "Asn" "Arg" "Arg" "Thr" "Thr" "Pro" "Val" "Stp"
##  [419] "Stp" "Pro" "Arg" "Ala" "Ser" "Pro" "Glu" "Asp" "Arg" "Gly" "Stp"
##  [430] "Stp" "Ala" "Arg" "Ser" "Pro" "Gly" "Ala" "Gly" "Arg" "Gly" "Gly"
##  [441] "Glu" "Thr" "Gln" "Thr" "Leu" "Arg" "Trp" "Glu" "Thr" "Phe" "Gln"
##  [452] "Lys" "Gln" "Lys" "Gln" "Lys" "Thr" "Lys" "Lys" "Thr" "Lys" "Lys"
##  [463] "Gln" "Lys" "Thr" "Lys" "Lys" "His" "Thr" "His" "Thr" "Lys" "Lys"
##  [474] "Glu" "Lys" "Lys" "His" "Asn" "Lys" "Stp" "Ile" "Leu" "Lys" "Lys"
##  [485] "Stp" "Thr" "Lys" "Tyr" "Lys" "Stp" "Asn" "Lys" "Glu" "Ala" "Lys"
##  [496] "Gln" "Gln" "Glu" "Met" "Trp" "Glu" "Asn" "Met" "Asn" "Glu" "Gly"
##  [507] "Stp" "Lys" "Gln" "Thr" "Leu" "Lys" "Lys" "Ser" "Glu" "Stp" "Asp"
##  [518] "Lys" "Lys" "Leu" "Lys" "Met" "Glu" "Asn" "Lys" "Ser" "Lys" "Stp"
##  [529] "Lys" "Cys" "Met" "Ile" "Ser" "His" "Val" "Pro" "Leu" "Phe" "Stp"
##  [540] "His" "Leu" "Met" "Lys" "Ile" "Asn" "Leu" "Asn" "Glu" "Lys" "Met"
##  [551] "Lys" "Gly" "Asn" "Gln" "Asp" "Asn" "Ile" "Lys" "Ala" "Lys" "Lys"
##  [562] "Lys" "Lys" "Met" "Stp" "Thr" "Glu" "Stp" "Lys" "Gly" "Asp" "Val"
##  [573] "Leu" "Cys" "Ile" "Phe" "Gln" "Gly" "Leu" "Cys" "Tyr" "Phe" "Phe"
##  [584] "Phe" "Phe" "Phe" "Leu" "Thr" "Arg" "Gly" "Glu" "Leu" "Leu" "Phe"
##  [595] "Cys" "Ser" "Leu" "Stp" "Pro" "Pro" "Ala" "Gly" "Pro" "Ala" "Ser"
##  [606] "Leu" "Gly" "Asp" "Trp" "Gly" "Ala" "Stp" "Leu" "Stp" "Gly" "Pro"
##  [617] "Gly" "Ala" "Stp" "Trp" "Ala" "Cys" "Ser" "His" "Cys" "Gln" "Val"
##  [628] "Pro" "Gly" "Ala" "Pro" "Gly" "Trp" "Val" "Pro" "Gln" "Glu" "Leu"
##  [639] "Gln" "Glu" "Gly" "Ser" "Glu" "Leu" "Glu" "Pro" "Ala" "Pro" "Pro"
##  [650] "Ser" "Ile" "Asp" "Gly" "Ala" "Ile" "Val" "Gly" "Leu" "Gln" "Val"
##  [661] "Thr" "Glu" "Pro" "Leu" "Ser" "Leu" "Leu" "Ser" "Val" "Stp" "Val"
##  [672] "Pro" "Gly" "Gly" "Gly" "Tyr" "Thr" "Trp" "Gly" "Leu" "Pro" "Gly"
##  [683] "Pro" "Stp" "Phe" "Pro" "Val" "Leu" "Asn" "Ala" "Pro" "Stp" "Pro"
##  [694] "Thr" "Val" "Met" "Thr" "Ser" "Stp" "Ala" "Leu" "Stp" "Lys" "Gly"
##  [705] "Lys" "Glu" "Stp" "Gly" "Gly" "Cys" "Arg" "Trp" "Leu" "Thr" "Lys"
##  [716] "Met" "Pro" "Glu" "Thr" "Pro" "Glu" "Ser" "Ser" "Gly" "Trp" "Ala"
##  [727] "Ser" "Trp" "Gly" "His" "Val" "Pro" "Lys" "Leu" "Leu" "Ser" "Leu"
##  [738] "Gly" "Ser" "Gly" "Asp" "Ala" "Thr" "Pro" "Pro" "Pro" "Gly" "Gly"
##  [749] "His" "Glu" "Thr" "Ala" "Leu" "Pro" "Pro" "His" "Pro" "Ser" "Pro"
##  [760] "Gln" "Gly" "His" "Leu" "Met" "Thr" "Leu" "Gly" "Arg" "Trp" "Trp"
##  [771] "Thr" "Pro" "Trp" "Leu" "Met" "Ser" "Pro" "Pro" "Val" "Pro" "Trp"
##  [782] "Glu" "Gly" "Gly" "Ser" "Leu" "Thr" "Leu" "Trp" "Gly" "Ser" "Leu"
##  [793] "Asp" "Ser" "Leu" "Met" "Pro" "Pro" "Trp" "Gly" "Pro" "Ala" "Gly"
##  [804] "Ser" "Thr" "Met" "Thr" "Leu" "Gln" "Lys" "Gly" "Phe" "Phe" "Leu"
##  [815] "Gln" "Lys" "Lys" "Lys" "Glu" "Lys" "Gln" "Val" "Val" "Ile" "Phe"
##  [826] "Phe" "Stp" "Stp" "Lys" "Asn" "His" "Stp" "Leu" "Stp" "Met" "Asn"
##  [837] "Val" "Asn" "Thr" "Lys" "Stp" "Val" "Asp" "Leu" "Leu" "Ala" "Stp"
##  [848] "Lys" "Ser" "Asp" "Ser" "Ile" "Phe" "Leu" "Leu" "Ile" "Leu" "Phe"
##  [859] "Gln" "Leu" "Stp" "Thr" "Val" "Lys" "Thr" "Lys" "Asn" "Gly" "Ala"
##  [870] "Gly" "Trp" "Gly" "Thr" "Stp" "Thr" "Leu" "Ala" "Gly" "Asn" "Leu"
##  [881] "Stp" "Stp" "Lys" "Lys" "Lys" "Gln" "Lys" "Thr" "Asn" "Met" "Gln"
##  [892] "Ile" "His" "Leu" "Gln" "Lys" "Gln" "Ser" "Lys" "Thr" "Val" "Val"
##  [903] "Stp" "Gly" "Glu" "Ser" "Trp" "Ala" "Trp" "Stp" "Leu" "Glu" "Gly"
##  [914] "Val" "Ala" "Glu" "Gly" "Pro" "Ser" "Glu" "Leu" "Gln" "Gly" "Val"
##  [925] "Ser" "Val" "Met" "Glu" "Stp" "Trp" "Leu" "Pro" "Gln" "Thr" "Stp"
##  [936] "Lys" "Val" "Leu" "Arg" "Met" "Gly" "Glu" "Asp" "Stp" "Ile" "Gln"
##  [947] "Gln" "Stp" "Lys" "Stp" "Pro" "His" "Thr" "Pro" "His" "Ala" "His"
##  [958] "Stp" "His" "Val" "His" "Thr" "His" "Met" "His" "Ser" "Pro" "Leu"
##  [969] "Ser" "Pro" "Ala" "Leu" "Gln" "Ser" "Leu" "Thr" "Gly" "Thr" "His"
##  [980] "Ser" "Val" "Ser" "Thr" "Leu" "Pro" "Ser" "His" "Thr" "Arg" "Pro"
##  [991] "Gly" "Ala" "Trp" "Leu" "Lys" "Gly" "Asn" "Trp" "Leu" "Met" "Pro"
## [1002] "Ser" "Lys" "Ala" "Met" "Asp" "Asp" "Asn" "Asn" "Ser" "Thr" "Leu"
## [1013] "Ala" "Phe" "Val" "Phe" "Ile" "His" "Asn" "Leu" "Pro" "Thr" "Glu"
## [1024] "His" "Thr" "His" "Glu" "His" "Thr" "His" "Ala" "His" "Met" "Pro"
## [1035] "Thr" "His" "Ala" "His" "Met" "Pro" "Thr" "His" "Thr" "His" "Thr"
## [1046] "Pro" "Leu" "Ala" "Cys" "Met" "Gly" "Stp" "Ala" "Pro" "Val" "Stp"
## [1057] "Asn" "Pro" "Gly" "Leu" "Asp" "Ser" "Gly" "Ile" "Pro" "Cys" "Cys"
## [1068] "Met" "Ala" "Ser" "Leu" "Gly" "Leu" "Asn" "Phe" "Pro" "Pro" "Met"
## [1079] "Stp" "Ala" "Cys" "Gly" "Leu" "Thr" "Gln" "Stp" "Ser" "Thr" "Lys"
## [1090] "Gly" "Pro" "Phe" "Leu" "Leu" "Tyr" "Val" "Ser" "Val" "Thr" "Stp"
## [1101] "Asp" "Leu" "Pro" "Pro" "Ala" "Pro" "Stp" "Met" "Cys" "Gln" "Gly"
## [1112] "Trp" "Pro" "Gly" "Gln" "Leu" "Pro" "Pro" "Ser" "Pro" "Gln" "Ala"
## [1123] "His" "His" "Gln" "Ser" "Ala" "Ser" "Gln" "Thr" "His" "Thr" "His"
## [1134] "Thr" "His" "Thr" "Met" "Tyr" "Leu" "Leu" "Thr" "Val" "Leu" "Pro"
## [1145] "Glu" "His" "Leu" "Pro" "Pro" "His" "Pro" "Met" "Ser" "Lys" "Gln"
## [1156] "Lys" "Tyr" "Thr" "His" "Val" "Ser" "Lys" "His" "Lys" "Ala" "Val"
## [1167] "Gln" "Ala" "Lys" "Stp" "Gly" "Lys" "Thr" "Gln" "Gly" "Ser" "Pro"
## [1178] "Lys" "Pro" "Phe" "Phe" "Thr" "Leu" "Cys" "Pro" "Leu" "Ala" "Ala"
## [1189] "Ile" "Met" "Glu" "Ser" "Stp" "Stp" "Gly" "Phe" "Leu" "Gly" "Stp"
## [1200] "Stp" "Ala" "Leu" "Pro" "Pro" "Gly" "Leu" "Pro" "Gln" "Cys" "Leu"
## [1211] "Trp" "Gly" "Ser" "Val" "Lys" "Lys" "Stp" "Ile" "Leu" "Trp" "Gly"
## [1222] "Leu" "Leu" "Gly" "Gly" "Leu" "Lys" "Ala" "Glu" "Gly" "Met" "Glu"
## [1233] "Stp" "Lys" "Ile" "Leu" "Ala" "Val" "Pro" "Ser" "Gln" "Cys" "Lys"
## [1244] "Asp" "Gln" "Pro" "Gln" "Lys" "Leu" "Asn" "Leu" "His" "His" "Stp"
## [1255] "Leu" "Lys" "Val" "Lys" "Gly" "Ile" "Leu" "Cys" "Phe" "Ser" "Pro"
## [1266] "Phe" "Phe" "Pro" "Stp" "Val" "Thr" "Stp" "Ala" "Ser" "Ser" "Asp"
## [1277] "Trp" "Gln" "Lys" "Ser" "Asn" "Ser" "Phe" "Pro" "Glu" "Leu" "Glu"
## [1288] "Ile" "Ser" "Glu" "Gln" "Ser" "Ala" "Ser" "Tyr" "Ser" "Gln" "Val"
## [1299] "Thr" "Glu" "Gly" "Gln" "Gly" "Glu" "Ala" "Pro" "Leu" "Pro" "Leu"
## [1310] "Pro" "Ala" "Ser" "Leu" "Pro" "Arg" "Phe" "Ala" "Phe" "Phe" "Leu"
## [1321] "Thr" "Pro" "Ala" "Phe" "Pro" "Glu" "Val" "Glu" "Leu" "Ser" "Gly"
## [1332] "Glu" "Phe" "Stp" "Stp" "Met" "Ala" "Ser" "Lys" "Ala" "Phe" "Trp"
## [1343] "Ala" "Cys" "Thr" "Ser" "His" "Leu" "Pro" "Phe" "Leu" "Ser" "Phe"
## [1354] "Ala" "Trp" "Glu" "Stp" "Lys" "Val" "Ile" "Phe" "Pro" "Gly" "Gln"
## [1365] "Gln" "Gly" "Ala" "Glu" "His" "Arg" "Pro" "Ala" "Gln" "Pro" "Stp"
## [1376] "Ser" "Thr" "Gly" "Gly" "Gly" "His" "Gly" "Pro" "Trp" "Gly" "Stp"
## [1387] "Thr" "Met" "Gly" "Asp" "Asn" "Ser" "Stp" "Cys" "Gly" "Asn" "Asn"
## [1398] "Asn" "Gln" "Val" "Ala" "Leu" "Ser" "Leu" "Gly" "Stp" "Asn" "Trp"
## [1409] "Thr" "Leu" "Pro" "Leu" "Ser" "His" "Pro" "Asn" "Leu" "Ala" "Arg"
## [1420] "His" "Pro" "Thr" "Stp" "Phe" "Gln" "Thr" "Stp" "Stp" "Asp" "Gln"
## [1431] "Gly" "Trp" "Glu" "Arg" "Stp" "Glu" "Lys" "Gly" "Gly" "Ser" "Pro"
## [1442] "Stp" "Lys" "Pro" "His" "Pro" "Ser" "Glu" "His" "Cys" "Leu" "Lys"
## [1453] "Stp" "Lys" "Thr" "Ser" "Ser" "Ser" "Ser" "Pro" "Asn" "Ser" "Gly"
## [1464] "Stp" "Ala" "Ser" "Gly" "Lys" "Ala" "Ile" "Ser" "Ala" "Ser" "Phe"
## [1475] "His" "Gly" "Ala" "Stp" "Pro" "Gly" "Phe" "Trp" "Val" "Cys" "Leu"
## [1486] "Lys" "Lys" "Ala" "Thr" "Gly" "Val" "Trp" "Gly" "Asp" "Ile" "Ala"
## [1497] "Met" "Ala" "Glu" "Lys" "Gly" "Leu" "Gly" "Gly" "Pro" "Glu" "Gly"
## [1508] "Stp" "Ser" "Gln" "Asp" "Arg" "Asn" "Cys" "Lys" "Gly" "Val" "Ala"
## [1519] "Ala" "Gln" "Gly" "Cys" "Gly" "Trp" "Leu" "Leu" "Met" "Ser" "Ser"
## [1530] "Ser" "Asp" "Gln" "Phe" "Lys" "Lys" "Leu" "Thr" "Ser" "Ile" "Tyr"
## [1541] "Phe" "Leu" "Gly" "Glu" "Ser" "Phe" "Phe" "Phe" "Phe" "Ser" "Asp"
## [1552] "Cys" "Stp" "Gln" "Lys" "Lys" "Asn" "Phe" "Lys" "Lys" "Gln" "Lys"
## [1563] "Thr" "Glu" "Lys" "Lys" "Asn" "Pro" "Gly" "Thr" "Trp" "Asn" "Lys"
## [1574] "Asp" "Phe" "Phe" "Phe" "Leu"

####################
#                  #
#    Exercise 6    #
#                  #
####################
library("seqinr")
seq1<-read.fasta(file="seq1.fasta")
sequences<-getSequence(seq1[[1]])
Amino<-getTrans(sequences, sens = "F", Frame = 1,numcode = 2,NAstring = "X", ambiguous = FALSE)
print(aaa(Amino))

##    [1] "Ser" "Phe" "Ser" "Phe" "Stp" "Lys" "Lys" "Asn" "Thr" "Ala" "Thr"
##   [12] "Gly" "Thr" "Val" "Ser" "Asp" "Leu" "Lys" "Stp" "Gln" "Ala" "Ser"
##   [23] "Ser" "Arg" "Val" "Ile" "Phe" "Met" "Ile" "Tyr" "Thr" "Leu" "Phe"
##   [34] "Arg" "Glu" "Leu" "Ser" "Tyr" "Leu" "Pro" "Phe" "Phe" "Met" "Thr"
##   [45] "Leu" "His" "Ile" "Leu" "Tyr" "Ser" "Tyr" "Met" "Tyr" "Pro" "Leu"
##   [56] "Tyr" "Stp" "Stp" "Trp" "Asn" "Asn" "Phe" "Tyr" "Phe" "Tyr" "Leu"
##   [67] "Phe" "Phe" "Leu" "Ala" "Leu" "Val" "Leu" "Ala" "Pro" "Ser" "His"
##   [78] "Thr" "Leu" "Ser" "Arg" "Glu" "Pro" "Glu" "Val" "Gly" "Trp" "Val"
##   [89] "Phe" "Met" "Stp" "Trp" "Stp" "Ile" "Met" "Gly" "Leu" "Phe" "Asp"
##  [100] "Arg" "Gly" "Val" "Gln" "Met" "Leu" "Leu" "Thr" "Thr" "Val" "Gly"
##  [111] "Ala" "Phe" "Ala" "Ala" "Phe" "Ser" "Leu" "Met" "Thr" "Met" "Ala"
##  [122] "Val" "Gly" "Thr" "Asp" "Tyr" "Trp" "Leu" "Tyr" "Ser" "Stp" "Gly"
##  [133] "Val" "Cys" "Lys" "Thr" "Lys" "Ser" "Val" "Ser" "Glu" "Asn" "Glu"
##  [144] "Thr" "Ser" "Lys" "Lys" "Asn" "Glu" "Glu" "Val" "Met" "Thr" "His"
##  [155] "Ser" "Gly" "Leu" "Trp" "Stp" "Thr" "Cys" "Cys" "Leu" "Glu" "Gly"
##  [166] "Asn" "Phe" "Lys" "Gly" "Leu" "Cys" "Lys" "Gln" "Ile" "Asp" "His"
##  [177] "Phe" "Pro" "Glu" "Asp" "Ala" "Asp" "Tyr" "Glu" "Ala" "Asp" "Thr"
##  [188] "Ala" "Glu" "Tyr" "Phe" "Leu" "Arg" "Ala" "Val" "Stp" "Ala" "Ser"
##  [199] "Ser" "Ile" "Phe" "Pro" "Ile" "Leu" "Ser" "Val" "Ile" "Leu" "Leu"
##  [210] "Phe" "Met" "Gly" "Gly" "Leu" "Cys" "Ile" "Ala" "Ala" "Ser" "Glu"
##  [221] "Phe" "Tyr" "Lys" "Thr" "Arg" "His" "Asn" "Ile" "Ile" "Leu" "Ser"
##  [232] "Ala" "Gly" "Ile" "Phe" "Phe" "Val" "Ser" "Ala" "Gly" "Leu" "Ser"
##  [243] "Asn" "Ile" "Ile" "Gly" "Ile" "Met" "Val" "Tyr" "Met" "Ser" "Ala"
##  [254] "Asn" "Ala" "Gly" "Asp" "Pro" "Ser" "Lys" "Ser" "Asp" "Ser" "Lys"
##  [265] "Lys" "Asn" "Ser" "Tyr" "Ser" "Tyr" "Gly" "Trp" "Ser" "Phe" "Tyr"
##  [276] "Phe" "Gly" "Ala" "Leu" "Ser" "Phe" "Ile" "Ile" "Ala" "Glu" "Met"
##  [287] "Val" "Gly" "Val" "Leu" "Ala" "Val" "His" "Met" "Phe" "Ile" "Asp"
##  [298] "Arg" "His" "Lys" "Gln" "Leu" "Arg" "Ala" "Thr" "Ala" "Arg" "Ala"
##  [309] "Thr" "Asp" "Tyr" "Leu" "Gln" "Ala" "Ser" "Ala" "Ile" "Thr" "Arg"
##  [320] "Ile" "Pro" "Ser" "Tyr" "Arg" "Tyr" "Arg" "Tyr" "Gln" "Arg" "Arg"
##  [331] "Ser" "Arg" "Ser" "Ser" "Ser" "Arg" "Ser" "Thr" "Glu" "Pro" "Ser"
##  [342] "His" "Ser" "Stp" "Asp" "Ala" "Ser" "Pro" "Val" "Gly" "Ile" "Lys"
##  [353] "Gly" "Phe" "Asn" "Thr" "Leu" "Pro" "Ser" "Thr" "Glu" "Ile" "Ser"
##  [364] "Met" "Tyr" "Thr" "Leu" "Ser" "Stp" "Asp" "Pro" "Leu" "Lys" "Ala"
##  [375] "Ala" "Thr" "Thr" "Pro" "Thr" "Ala" "Thr" "Tyr" "Asn" "Ser" "Asp"
##  [386] "Stp" "Asp" "Asn" "Ser" "Phe" "Leu" "Gln" "Val" "His" "Asn" "Cys"
##  [397] "Ile" "Gln" "Lys" "Glu" "Asn" "Lys" "Asp" "Ser" "Leu" "His" "Ser"
##  [408] "Asn" "Thr" "Ala" "Asn" "Arg" "Arg" "Thr" "Thr" "Pro" "Val" "Stp"
##  [419] "Stp" "Pro" "Arg" "Ala" "Ser" "Pro" "Glu" "Asp" "Arg" "Gly" "Stp"
##  [430] "Stp" "Ala" "Arg" "Ser" "Pro" "Gly" "Ala" "Gly" "Arg" "Gly" "Gly"
##  [441] "Glu" "Thr" "Gln" "Thr" "Leu" "Arg" "Trp" "Glu" "Thr" "Phe" "Gln"
##  [452] "Lys" "Gln" "Lys" "Gln" "Lys" "Thr" "Lys" "Lys" "Thr" "Lys" "Lys"
##  [463] "Gln" "Lys" "Thr" "Lys" "Lys" "His" "Thr" "His" "Thr" "Lys" "Lys"
##  [474] "Glu" "Lys" "Lys" "His" "Asn" "Lys" "Stp" "Ile" "Leu" "Lys" "Lys"
##  [485] "Stp" "Thr" "Lys" "Tyr" "Lys" "Stp" "Asn" "Lys" "Glu" "Ala" "Lys"
##  [496] "Gln" "Gln" "Glu" "Met" "Trp" "Glu" "Asn" "Met" "Asn" "Glu" "Gly"
##  [507] "Stp" "Lys" "Gln" "Thr" "Leu" "Lys" "Lys" "Ser" "Glu" "Stp" "Asp"
##  [518] "Lys" "Lys" "Leu" "Lys" "Met" "Glu" "Asn" "Lys" "Ser" "Lys" "Stp"
##  [529] "Lys" "Cys" "Met" "Ile" "Ser" "His" "Val" "Pro" "Leu" "Phe" "Stp"
##  [540] "His" "Leu" "Met" "Lys" "Ile" "Asn" "Leu" "Asn" "Glu" "Lys" "Met"
##  [551] "Lys" "Gly" "Asn" "Gln" "Asp" "Asn" "Ile" "Lys" "Ala" "Lys" "Lys"
##  [562] "Lys" "Lys" "Met" "Stp" "Thr" "Glu" "Stp" "Lys" "Gly" "Asp" "Val"
##  [573] "Leu" "Cys" "Ile" "Phe" "Gln" "Gly" "Leu" "Cys" "Tyr" "Phe" "Phe"
##  [584] "Phe" "Phe" "Phe" "Leu" "Thr" "Arg" "Gly" "Glu" "Leu" "Leu" "Phe"
##  [595] "Cys" "Ser" "Leu" "Stp" "Pro" "Pro" "Ala" "Gly" "Pro" "Ala" "Ser"
##  [606] "Leu" "Gly" "Asp" "Trp" "Gly" "Ala" "Stp" "Leu" "Stp" "Gly" "Pro"
##  [617] "Gly" "Ala" "Stp" "Trp" "Ala" "Cys" "Ser" "His" "Cys" "Gln" "Val"
##  [628] "Pro" "Gly" "Ala" "Pro" "Gly" "Trp" "Val" "Pro" "Gln" "Glu" "Leu"
##  [639] "Gln" "Glu" "Gly" "Ser" "Glu" "Leu" "Glu" "Pro" "Ala" "Pro" "Pro"
##  [650] "Ser" "Ile" "Asp" "Gly" "Ala" "Ile" "Val" "Gly" "Leu" "Gln" "Val"
##  [661] "Thr" "Glu" "Pro" "Leu" "Ser" "Leu" "Leu" "Ser" "Val" "Stp" "Val"
##  [672] "Pro" "Gly" "Gly" "Gly" "Tyr" "Thr" "Trp" "Gly" "Leu" "Pro" "Gly"
##  [683] "Pro" "Stp" "Phe" "Pro" "Val" "Leu" "Asn" "Ala" "Pro" "Stp" "Pro"
##  [694] "Thr" "Val" "Met" "Thr" "Ser" "Stp" "Ala" "Leu" "Stp" "Lys" "Gly"
##  [705] "Lys" "Glu" "Stp" "Gly" "Gly" "Cys" "Arg" "Trp" "Leu" "Thr" "Lys"
##  [716] "Met" "Pro" "Glu" "Thr" "Pro" "Glu" "Ser" "Ser" "Gly" "Trp" "Ala"
##  [727] "Ser" "Trp" "Gly" "His" "Val" "Pro" "Lys" "Leu" "Leu" "Ser" "Leu"
##  [738] "Gly" "Ser" "Gly" "Asp" "Ala" "Thr" "Pro" "Pro" "Pro" "Gly" "Gly"
##  [749] "His" "Glu" "Thr" "Ala" "Leu" "Pro" "Pro" "His" "Pro" "Ser" "Pro"
##  [760] "Gln" "Gly" "His" "Leu" "Met" "Thr" "Leu" "Gly" "Arg" "Trp" "Trp"
##  [771] "Thr" "Pro" "Trp" "Leu" "Met" "Ser" "Pro" "Pro" "Val" "Pro" "Trp"
##  [782] "Glu" "Gly" "Gly" "Ser" "Leu" "Thr" "Leu" "Trp" "Gly" "Ser" "Leu"
##  [793] "Asp" "Ser" "Leu" "Met" "Pro" "Pro" "Trp" "Gly" "Pro" "Ala" "Gly"
##  [804] "Ser" "Thr" "Met" "Thr" "Leu" "Gln" "Lys" "Gly" "Phe" "Phe" "Leu"
##  [815] "Gln" "Lys" "Lys" "Lys" "Glu" "Lys" "Gln" "Val" "Val" "Ile" "Phe"
##  [826] "Phe" "Stp" "Stp" "Lys" "Asn" "His" "Stp" "Leu" "Stp" "Met" "Asn"
##  [837] "Val" "Asn" "Thr" "Lys" "Stp" "Val" "Asp" "Leu" "Leu" "Ala" "Stp"
##  [848] "Lys" "Ser" "Asp" "Ser" "Ile" "Phe" "Leu" "Leu" "Ile" "Leu" "Phe"
##  [859] "Gln" "Leu" "Stp" "Thr" "Val" "Lys" "Thr" "Lys" "Asn" "Gly" "Ala"
##  [870] "Gly" "Trp" "Gly" "Thr" "Stp" "Thr" "Leu" "Ala" "Gly" "Asn" "Leu"
##  [881] "Stp" "Stp" "Lys" "Lys" "Lys" "Gln" "Lys" "Thr" "Asn" "Met" "Gln"
##  [892] "Ile" "His" "Leu" "Gln" "Lys" "Gln" "Ser" "Lys" "Thr" "Val" "Val"
##  [903] "Stp" "Gly" "Glu" "Ser" "Trp" "Ala" "Trp" "Stp" "Leu" "Glu" "Gly"
##  [914] "Val" "Ala" "Glu" "Gly" "Pro" "Ser" "Glu" "Leu" "Gln" "Gly" "Val"
##  [925] "Ser" "Val" "Met" "Glu" "Stp" "Trp" "Leu" "Pro" "Gln" "Thr" "Stp"
##  [936] "Lys" "Val" "Leu" "Arg" "Met" "Gly" "Glu" "Asp" "Stp" "Ile" "Gln"
##  [947] "Gln" "Stp" "Lys" "Stp" "Pro" "His" "Thr" "Pro" "His" "Ala" "His"
##  [958] "Stp" "His" "Val" "His" "Thr" "His" "Met" "His" "Ser" "Pro" "Leu"
##  [969] "Ser" "Pro" "Ala" "Leu" "Gln" "Ser" "Leu" "Thr" "Gly" "Thr" "His"
##  [980] "Ser" "Val" "Ser" "Thr" "Leu" "Pro" "Ser" "His" "Thr" "Arg" "Pro"
##  [991] "Gly" "Ala" "Trp" "Leu" "Lys" "Gly" "Asn" "Trp" "Leu" "Met" "Pro"
## [1002] "Ser" "Lys" "Ala" "Met" "Asp" "Asp" "Asn" "Asn" "Ser" "Thr" "Leu"
## [1013] "Ala" "Phe" "Val" "Phe" "Ile" "His" "Asn" "Leu" "Pro" "Thr" "Glu"
## [1024] "His" "Thr" "His" "Glu" "His" "Thr" "His" "Ala" "His" "Met" "Pro"
## [1035] "Thr" "His" "Ala" "His" "Met" "Pro" "Thr" "His" "Thr" "His" "Thr"
## [1046] "Pro" "Leu" "Ala" "Cys" "Met" "Gly" "Stp" "Ala" "Pro" "Val" "Stp"
## [1057] "Asn" "Pro" "Gly" "Leu" "Asp" "Ser" "Gly" "Ile" "Pro" "Cys" "Cys"
## [1068] "Met" "Ala" "Ser" "Leu" "Gly" "Leu" "Asn" "Phe" "Pro" "Pro" "Met"
## [1079] "Stp" "Ala" "Cys" "Gly" "Leu" "Thr" "Gln" "Stp" "Ser" "Thr" "Lys"
## [1090] "Gly" "Pro" "Phe" "Leu" "Leu" "Tyr" "Val" "Ser" "Val" "Thr" "Stp"
## [1101] "Asp" "Leu" "Pro" "Pro" "Ala" "Pro" "Stp" "Met" "Cys" "Gln" "Gly"
## [1112] "Trp" "Pro" "Gly" "Gln" "Leu" "Pro" "Pro" "Ser" "Pro" "Gln" "Ala"
## [1123] "His" "His" "Gln" "Ser" "Ala" "Ser" "Gln" "Thr" "His" "Thr" "His"
## [1134] "Thr" "His" "Thr" "Met" "Tyr" "Leu" "Leu" "Thr" "Val" "Leu" "Pro"
## [1145] "Glu" "His" "Leu" "Pro" "Pro" "His" "Pro" "Met" "Ser" "Lys" "Gln"
## [1156] "Lys" "Tyr" "Thr" "His" "Val" "Ser" "Lys" "His" "Lys" "Ala" "Val"
## [1167] "Gln" "Ala" "Lys" "Stp" "Gly" "Lys" "Thr" "Gln" "Gly" "Ser" "Pro"
## [1178] "Lys" "Pro" "Phe" "Phe" "Thr" "Leu" "Cys" "Pro" "Leu" "Ala" "Ala"
## [1189] "Ile" "Met" "Glu" "Ser" "Stp" "Stp" "Gly" "Phe" "Leu" "Gly" "Stp"
## [1200] "Stp" "Ala" "Leu" "Pro" "Pro" "Gly" "Leu" "Pro" "Gln" "Cys" "Leu"
## [1211] "Trp" "Gly" "Ser" "Val" "Lys" "Lys" "Stp" "Ile" "Leu" "Trp" "Gly"
## [1222] "Leu" "Leu" "Gly" "Gly" "Leu" "Lys" "Ala" "Glu" "Gly" "Met" "Glu"
## [1233] "Stp" "Lys" "Ile" "Leu" "Ala" "Val" "Pro" "Ser" "Gln" "Cys" "Lys"
## [1244] "Asp" "Gln" "Pro" "Gln" "Lys" "Leu" "Asn" "Leu" "His" "His" "Stp"
## [1255] "Leu" "Lys" "Val" "Lys" "Gly" "Ile" "Leu" "Cys" "Phe" "Ser" "Pro"
## [1266] "Phe" "Phe" "Pro" "Stp" "Val" "Thr" "Stp" "Ala" "Ser" "Ser" "Asp"
## [1277] "Trp" "Gln" "Lys" "Ser" "Asn" "Ser" "Phe" "Pro" "Glu" "Leu" "Glu"
## [1288] "Ile" "Ser" "Glu" "Gln" "Ser" "Ala" "Ser" "Tyr" "Ser" "Gln" "Val"
## [1299] "Thr" "Glu" "Gly" "Gln" "Gly" "Glu" "Ala" "Pro" "Leu" "Pro" "Leu"
## [1310] "Pro" "Ala" "Ser" "Leu" "Pro" "Arg" "Phe" "Ala" "Phe" "Phe" "Leu"
## [1321] "Thr" "Pro" "Ala" "Phe" "Pro" "Glu" "Val" "Glu" "Leu" "Ser" "Gly"
## [1332] "Glu" "Phe" "Stp" "Stp" "Met" "Ala" "Ser" "Lys" "Ala" "Phe" "Trp"
## [1343] "Ala" "Cys" "Thr" "Ser" "His" "Leu" "Pro" "Phe" "Leu" "Ser" "Phe"
## [1354] "Ala" "Trp" "Glu" "Stp" "Lys" "Val" "Ile" "Phe" "Pro" "Gly" "Gln"
## [1365] "Gln" "Gly" "Ala" "Glu" "His" "Arg" "Pro" "Ala" "Gln" "Pro" "Stp"
## [1376] "Ser" "Thr" "Gly" "Gly" "Gly" "His" "Gly" "Pro" "Trp" "Gly" "Stp"
## [1387] "Thr" "Met" "Gly" "Asp" "Asn" "Ser" "Stp" "Cys" "Gly" "Asn" "Asn"
## [1398] "Asn" "Gln" "Val" "Ala" "Leu" "Ser" "Leu" "Gly" "Stp" "Asn" "Trp"
## [1409] "Thr" "Leu" "Pro" "Leu" "Ser" "His" "Pro" "Asn" "Leu" "Ala" "Arg"
## [1420] "His" "Pro" "Thr" "Stp" "Phe" "Gln" "Thr" "Stp" "Stp" "Asp" "Gln"
## [1431] "Gly" "Trp" "Glu" "Arg" "Stp" "Glu" "Lys" "Gly" "Gly" "Ser" "Pro"
## [1442] "Stp" "Lys" "Pro" "His" "Pro" "Ser" "Glu" "His" "Cys" "Leu" "Lys"
## [1453] "Stp" "Lys" "Thr" "Ser" "Ser" "Ser" "Ser" "Pro" "Asn" "Ser" "Gly"
## [1464] "Stp" "Ala" "Ser" "Gly" "Lys" "Ala" "Ile" "Ser" "Ala" "Ser" "Phe"
## [1475] "His" "Gly" "Ala" "Stp" "Pro" "Gly" "Phe" "Trp" "Val" "Cys" "Leu"
## [1486] "Lys" "Lys" "Ala" "Thr" "Gly" "Val" "Trp" "Gly" "Asp" "Ile" "Ala"
## [1497] "Met" "Ala" "Glu" "Lys" "Gly" "Leu" "Gly" "Gly" "Pro" "Glu" "Gly"
## [1508] "Stp" "Ser" "Gln" "Asp" "Arg" "Asn" "Cys" "Lys" "Gly" "Val" "Ala"
## [1519] "Ala" "Gln" "Gly" "Cys" "Gly" "Trp" "Leu" "Leu" "Met" "Ser" "Ser"
## [1530] "Ser" "Asp" "Gln" "Phe" "Lys" "Lys" "Leu" "Thr" "Ser" "Ile" "Tyr"
## [1541] "Phe" "Leu" "Gly" "Glu" "Ser" "Phe" "Phe" "Phe" "Phe" "Ser" "Asp"
## [1552] "Cys" "Stp" "Gln" "Lys" "Lys" "Asn" "Phe" "Lys" "Lys" "Gln" "Lys"
## [1563] "Thr" "Glu" "Lys" "Lys" "Asn" "Pro" "Gly" "Thr" "Trp" "Asn" "Lys"
## [1574] "Asp" "Phe" "Phe" "Phe" "Leu"

####################
#                  #
#    Exercise 7    #
#                  #
####################

library("seqinr")
seq1<-read.fasta(file="seq1.fasta")
sequences<-getSequence(seq1[[1]])
Amino<-getTrans(sequences, sens = "F", Frame = 1,numcode = 2,NAstring = "X", ambiguous = FALSE)
AminoSeq<-c2s(Amino)
print(AminoSeq)

## [1] "SFSF*KKNTATGTVSDLK*QASSRVIFMIYTLFRELSYLPFFMTLHILYSYMYPLY**WNNFYFYLFFLALVLAPSHTLSREPEVGWVFM*W*IMGLFDRGVQMLLTTVGAFAAFSLMTMAVGTDYWLYS*GVCKTKSVSENETSKKNEEVMTHSGLW*TCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAV*ASSIFPILSVILLFMGGLCIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIMVYMSANAGDPSKSDSKKNSYSYGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLRATARATDYLQASAITRIPSYRYRYQRRSRSSSRSTEPSHS*DASPVGIKGFNTLPSTEISMYTLS*DPLKAATTPTATYNSD*DNSFLQVHNCIQKENKDSLHSNTANRRTTPV**PRASPEDRG**ARSPGAGRGGETQTLRWETFQKQKQKTKKTKKQKTKKHTHTKKEKKHNK*ILKK*TKYK*NKEAKQQEMWENMNEG*KQTLKKSE*DKKLKMENKSK*KCMISHVPLF*HLMKINLNEKMKGNQDNIKAKKKKM*TE*KGDVLCIFQGLCYFFFFFLTRGELLFCSL*PPAGPASLGDWGA*L*GPGA*WACSHCQVPGAPGWVPQELQEGSELEPAPPSIDGAIVGLQVTEPLSLLSV*VPGGGYTWGLPGP*FPVLNAP*PTVMTS*AL*KGKE*GGCRWLTKMPETPESSGWASWGHVPKLLSLGSGDATPPPGGHETALPPHPSPQGHLMTLGRWWTPWLMSPPVPWEGGSLTLWGSLDSLMPPWGPAGSTMTLQKGFFLQKKKEKQVVIFF**KNH*L*MNVNTK*VDLLA*KSDSIFLLILFQL*TVKTKNGAGWGT*TLAGNL**KKKQKTNMQIHLQKQSKTVV*GESWAW*LEGVAEGPSELQGVSVME*WLPQT*KVLRMGED*IQQ*K*PHTPHAH*HVHTHMHSPLSPALQSLTGTHSVSTLPSHTRPGAWLKGNWLMPSKAMDDNNSTLAFVFIHNLPTEHTHEHTHAHMPTHAHMPTHTHTPLACMG*APV*NPGLDSGIPCCMASLGLNFPPM*ACGLTQ*STKGPFLLYVSVT*DLPPAP*MCQGWPGQLPPSPQAHHQSASQTHTHTHTMYLLTVLPEHLPPHPMSKQKYTHVSKHKAVQAK*GKTQGSPKPFFTLCPLAAIMES**GFLG**ALPPGLPQCLWGSVKK*ILWGLLGGLKAEGME*KILAVPSQCKDQPQKLNLHH*LKVKGILCFSPFFP*VT*ASSDWQKSNSFPELEISEQSASYSQVTEGQGEAPLPLPASLPRFAFFLTPAFPEVELSGEF**MASKAFWACTSHLPFLSFAWE*KVIFPGQQGAEHRPAQP*STGGGHGPWG*TMGDNS*CGNNNQVALSLG*NWTLPLSHPNLARHPT*FQT**DQGWER*EKGGSP*KPHPSEHCLK*KTSSSSPNSG*ASGKAISASFHGA*PGFWVCLKKATGVWGDIAMAEKGLGGPEG*SQDRNCKGVAAQGCGWLLMSSSDQFKKLTSIYFLGESFFFFSDC*QKKNFKKQKTEKKNPGTWNKDFFFL"

####################
#                  #
#    Exercise 8    #
#                  #
####################

library("seqinr")
seq1<-read.fasta(file="seq1.fasta")
sequences<-getSequence(seq1[[1]])
Amino<-getTrans(sequences, sens = "F", NAstring = "X", ambiguous = FALSE)
print("Iso Electric Point")

## [1] "Iso Electric Point"

pi<-computePI(Amino)
print(pi)

## [1] 10.01812

####################
#                  #
#    Exercise 9    #
#                  #
####################

library("seqinr")
seq1<-read.fasta(file="seq1.fasta")
sequences<-getSequence(seq1[[1]])
Amino<-getTrans(sequences, sens = "F", Frame = 1,numcode = 2,NAstring = "X", ambiguous = FALSE)
print("Molecular Weight")

## [1] "Molecular Weight"

print(pmw(Amino))

## [1] 164719.6

####################
#                  #
#    Exercise 10   #
#                  #
####################

library("seqinr")
seq1<-read.fasta(file="seq1.fasta")
sequences<-getSequence(seq1[[1]])
Amino<-getTrans(sequences, sens = "F", NAstring = "X", ambiguous = FALSE)
AAstat(Amino,plot=TRUE)

## $Compo
## 
##   *   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T 
##  38 100  29  40  69  77 125  60  65 119 145  30  52 114  64  95 133 102 
##   V   W   Y 
##  64  26  31 
## 
## $Prop
## $Prop$Tiny
## [1] 0.3098859
## 
## $Prop$Small
## [1] 0.4809886
## 
## $Prop$Aliphatic
## [1] 0.1736375
## 
## $Prop$Aromatic
## [1] 0.1229404
## 
## $Prop$Non.polar
## [1] 0.5107731
## 
## $Prop$Polar
## [1] 0.4651458
## 
## $Prop$Charged
## [1] 0.2427123
## 
## $Prop$Basic
## [1] 0.1736375
## 
## $Prop$Acidic
## [1] 0.06907478
## 
## 
## $Pi
## [1] 10.01812

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