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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