Scrape Sequences

Followed the code to get the sequences from GenBank.

library(ape)
seq1 <- paste("JQ", seq(983161, 983255), sep = "") 
sequences <- read.GenBank(seq1,
                          seq.names = seq1,
                          species.names = TRUE,
                          as.character = TRUE)
write.dna(sequences, "fish.fasta", format = "fasta")

Used the accession sequence downloaded from NCBI to create an input for Salmo trutta.

accessions <- read.table("~/Desktop/BIN510-assignments/sequence.seq", stringsAsFactors = FALSE)
accessions

##             V1
## 1   JX960942.1
## 2   JX960943.1
## 3   JX960944.1
## 4   JX960946.1
## 5   OM283720.1
## 6   OM283733.1
## 7   OM283758.1
## 8   OM283759.1
## 9   OM283760.1
## 10  OM283761.1
## 11  OM283762.1
## 12  OM283763.1
## 13  OM283764.1
## 14  OM283765.1
## 15  OM283766.1
## 16  OM283767.1
## 17  OM283771.1
## 18  OM283772.1
## 19  OM283773.1
## 20  OM283774.1
## 21  OM283780.1
## 22  OM283781.1
## 23  OM283782.1
## 24  OM283783.1
## 25  OM283784.1
## 26  OM283788.1
## 27  OM283789.1
## 28  OM283790.1
## 29  OM283791.1
## 30  OM283792.1
## 31  OM283793.1
## 32  OM283800.1
## 33  OM283801.1
## 34  OM283802.1
## 35  OM283803.1
## 36  OM283804.1
## 37  OM283810.1
## 38  OM283811.1
## 39  OM283812.1
## 40  OM283813.1
## 41  OM286738.1
## 42  OM286739.1
## 43  OM286740.1
## 44  OM286741.1
## 45  OM286742.1
## 46  OM286743.1
## 47  OM286744.1
## 48  OM286745.1
## 49  OM286746.1
## 50  OM286748.1
## 51  OM286750.1
## 52  OM286751.1
## 53  OM286875.1
## 54  OM286876.1
## 55  OM286877.1
## 56  OM286878.1
## 57  OM286879.1
## 58  OM287397.1
## 59  OM289846.1
## 60  OM289847.1
## 61  OM289848.1
## 62  OM289849.1
## 63  OM289850.1
## 64  OM289851.1
## 65  OM289852.1
## 66  OM289853.1
## 67  OM289854.1
## 68  OM289855.1
## 69  OM289856.1
## 70  OM289857.1
## 71  OM289858.1
## 72  OM289859.1
## 73  OM289860.1
## 74  OM289861.1
## 75  OM289872.1
## 76  OM289873.1
## 77  OM289874.1
## 78  OM289883.1
## 79  OM289884.1
## 80  OM289885.1
## 81  OM289886.1
## 82  OM289887.1
## 83  OM289888.1
## 84  OM289889.1
## 85  OM289890.1
## 86  OM289891.1
## 87  OM289892.1
## 88  OM289893.1
## 89  OM289894.1
## 90  OM289895.1
## 91  OM289896.1
## 92  OM289897.1
## 93  OM289898.1
## 94  OM289899.1
## 95  OM289900.1
## 96  OM289901.1
## 97  OM289902.1
## 98  OM289903.1
## 99  OM289904.1
## 100 OM289905.1
## 101 OM289906.1
## 102 OM289907.1
## 103 OM289908.1
## 104 OM289909.1
## 105 OM289910.1
## 106 OM289911.1
## 107 OM289912.1
## 108 OM289913.1
## 109 OM289914.1
## 110 OM289915.1
## 111 OM289916.1
## 112 OM289917.1
## 113 OM289944.1
## 114 OM289945.1
## 115 OM289946.1
## 116 OM289947.1
## 117 OM292605.1
## 118 OM292606.1
## 119 OM292770.1
## 120 OM292771.1
## 121 OM292772.1
## 122 OM292773.1
## 123 OM292774.1
## 124 OM292775.1
## 125 OM292776.1
## 126 OM292777.1
## 127 OM292778.1
## 128 OM292779.1
## 129 OM292780.1
## 130 OM292781.1
## 131 OM292782.1
## 132 OM292783.1
## 133 OM292784.1
## 134 OM292785.1
## 135 OM292786.1
## 136 OM292787.1
## 137 OM292788.1
## 138 OM292789.1
## 139 OM292790.1
## 140 OM292791.1
## 141 OM292792.1
## 142 OM292793.1
## 143 OM292794.1
## 144 OM292795.1
## 145 OM292796.1
## 146 OM292797.1
## 147 OM292798.1
## 148 OM295688.1
## 149 OM295689.1
## 150 OM295690.1
## 151 OM295691.1
## 152 OM295692.1
## 153 OM295693.1
## 154 OM295694.1
## 155 OM295695.1
## 156 OM295696.1
## 157 OM295697.1
## 158 OM295698.1
## 159 OM295699.1
## 160 OM321445.1
## 161 OM321446.1
## 162 OM321447.1
## 163 OM321448.1
## 164 OM321449.1
## 165 OM321450.1
## 166 OM321451.1
## 167 OM321452.1
## 168 OM321453.1
## 169 OM321454.1
## 170 OM321455.1
## 171 OM321460.1
## 172 OM321461.1
## 173 OM321462.1
## 174 OM321463.1
## 175 OM321464.1
## 176 OM321465.1
## 177 OM321466.1
## 178 OM321467.1
## 179 OM321468.1
## 180 OM321469.1
## 181 OM321470.1
## 182 OM321471.1
## 183 OM321472.1
## 184 OM321473.1
## 185 OM321474.1
## 186 OM321475.1
## 187 OM327611.1
## 188 OM327612.1
## 189 OM327613.1
## 190 OM327614.1
## 191 OM327615.1
## 192 OM327616.1
## 193 OM327617.1
## 194 OM327618.1
## 195 OM327619.1
## 196 OM327620.1
## 197 OM327624.1
## 198 OM327631.1
## 199 PV918954.1
## 200 PV918955.1
## 201 PV918956.1
## 202 PV918957.1
## 203 PV918958.1
## 204 PV918959.1
## 205 PV918962.1
## 206 PV918963.1
## 207 PV918964.1
## 208 PV918965.1
## 209 PV918966.1
## 210 PV918967.1
## 211 PV918968.1
## 212 PV918969.1
## 213 PV918970.1
## 214 PV918971.1
## 215 PV919004.1
## 216 PV919005.1
## 217 PV919006.1
## 218 PV919007.1
## 219 PV919008.1
## 220 PV919010.1
## 221 PV919011.1
## 222 PV919012.1
## 223 PV919013.1
## 224 PV919014.1
## 225 PV919015.1
## 226 PV919016.1
## 227 PV919017.1
## 228 PV919018.1
## 229 PV919019.1
## 230 PV919020.1
## 231 PV919021.1
## 232 PV919022.1
## 233 PV919023.1
## 234 PV919024.1
## 235 PV919038.1
## 236 PV919039.1
## 237 PV919040.1
## 238 PV919041.1
## 239 PV919042.1
## 240 PV919043.1
## 241 PV919044.1
## 242 PV919045.1
## 243 PV919046.1
## 244 PV919047.1
## 245 PV919048.1
## 246 PV919049.1
## 247 PV919050.1
## 248 PV919051.1
## 249 PV919063.1
## 250 PV919064.1
## 251 PV919065.1
## 252 PV919135.1
## 253 PV919136.1
## 254 PV919137.1
## 255 PV919138.1
## 256 PV919139.1
## 257 PV919140.1
## 258 PV919141.1
## 259 PV919142.1
## 260 PV919149.1
## 261 PV919150.1
## 262 PV919151.1
## 263 PV919152.1
## 264 PV919461.1
## 265 PV919462.1
## 266 PV919463.1
## 267 PV919473.1
## 268 PV919474.1
## 269 PV919515.1
## 270 PV919516.1
## 271 PV928216.1
## 272 PV928217.1
## 273 PV928218.1
## 274 PV928219.1
## 275 PV928220.1
## 276 PV928228.1
## 277 PV928229.1
## 278 PV928230.1
## 279 PV928231.1
## 280 PV928232.1
## 281 PV928233.1
## 282 PV928234.1
## 283 PV928261.1
## 284 PV928262.1
## 285 PV928263.1
## 286 PV928264.1
## 287 PV928265.1
## 288 PV928266.1
## 289 PV928267.1
## 290 PV928268.1
## 291 PV928269.1
## 292 PV928270.1
## 293 PV928271.1
## 294 PV928272.1
## 295 PV928273.1
## 296 PV928300.1
## 297 PV928305.1
## 298 PV928306.1
## 299 PV928307.1
## 300 PV928668.1
## 301 PV928669.1
## 302 PV928743.1
## 303 PV928744.1
## 304 PV928745.1
## 305 PV928944.1
## 306 PV928945.1
## 307 PV928948.1
## 308 PV928949.1
## 309 PV928952.1
## 310 PV928953.1
## 311 PV928955.1
## 312 PV928996.1
## 313 PV928998.1
## 314 PV929010.1
## 315 PV929014.1
## 316 PV929015.1
## 317 PV929016.1
## 318 PV929020.1
## 319 PV929023.1
## 320 PV929024.1
## 321 PV929025.1
## 322 PV929026.1
## 323 PV929027.1
## 324 PV929048.1
## 325 PV929049.1
## 326 PV929050.1
## 327 PV929051.1
## 328 PV929055.1
## 329 PV929056.1
## 330 PV929057.1
## 331 PV929058.1
## 332 PV929059.1
## 333 PV929060.1
## 334 PV929061.1
## 335 PV929062.1
## 336 PV929063.1
## 337 PV929064.1
## 338 PV929065.1

nrow(accessions)

## [1] 338

head(accessions)

##           V1
## 1 JX960942.1
## 2 JX960943.1
## 3 JX960944.1
## 4 JX960946.1
## 5 OM283720.1
## 6 OM283733.1

accession_numbers <- accessions$V1
accession_numbers

##   [1] "JX960942.1" "JX960943.1" "JX960944.1" "JX960946.1" "OM283720.1"
##   [6] "OM283733.1" "OM283758.1" "OM283759.1" "OM283760.1" "OM283761.1"
##  [11] "OM283762.1" "OM283763.1" "OM283764.1" "OM283765.1" "OM283766.1"
##  [16] "OM283767.1" "OM283771.1" "OM283772.1" "OM283773.1" "OM283774.1"
##  [21] "OM283780.1" "OM283781.1" "OM283782.1" "OM283783.1" "OM283784.1"
##  [26] "OM283788.1" "OM283789.1" "OM283790.1" "OM283791.1" "OM283792.1"
##  [31] "OM283793.1" "OM283800.1" "OM283801.1" "OM283802.1" "OM283803.1"
##  [36] "OM283804.1" "OM283810.1" "OM283811.1" "OM283812.1" "OM283813.1"
##  [41] "OM286738.1" "OM286739.1" "OM286740.1" "OM286741.1" "OM286742.1"
##  [46] "OM286743.1" "OM286744.1" "OM286745.1" "OM286746.1" "OM286748.1"
##  [51] "OM286750.1" "OM286751.1" "OM286875.1" "OM286876.1" "OM286877.1"
##  [56] "OM286878.1" "OM286879.1" "OM287397.1" "OM289846.1" "OM289847.1"
##  [61] "OM289848.1" "OM289849.1" "OM289850.1" "OM289851.1" "OM289852.1"
##  [66] "OM289853.1" "OM289854.1" "OM289855.1" "OM289856.1" "OM289857.1"
##  [71] "OM289858.1" "OM289859.1" "OM289860.1" "OM289861.1" "OM289872.1"
##  [76] "OM289873.1" "OM289874.1" "OM289883.1" "OM289884.1" "OM289885.1"
##  [81] "OM289886.1" "OM289887.1" "OM289888.1" "OM289889.1" "OM289890.1"
##  [86] "OM289891.1" "OM289892.1" "OM289893.1" "OM289894.1" "OM289895.1"
##  [91] "OM289896.1" "OM289897.1" "OM289898.1" "OM289899.1" "OM289900.1"
##  [96] "OM289901.1" "OM289902.1" "OM289903.1" "OM289904.1" "OM289905.1"
## [101] "OM289906.1" "OM289907.1" "OM289908.1" "OM289909.1" "OM289910.1"
## [106] "OM289911.1" "OM289912.1" "OM289913.1" "OM289914.1" "OM289915.1"
## [111] "OM289916.1" "OM289917.1" "OM289944.1" "OM289945.1" "OM289946.1"
## [116] "OM289947.1" "OM292605.1" "OM292606.1" "OM292770.1" "OM292771.1"
## [121] "OM292772.1" "OM292773.1" "OM292774.1" "OM292775.1" "OM292776.1"
## [126] "OM292777.1" "OM292778.1" "OM292779.1" "OM292780.1" "OM292781.1"
## [131] "OM292782.1" "OM292783.1" "OM292784.1" "OM292785.1" "OM292786.1"
## [136] "OM292787.1" "OM292788.1" "OM292789.1" "OM292790.1" "OM292791.1"
## [141] "OM292792.1" "OM292793.1" "OM292794.1" "OM292795.1" "OM292796.1"
## [146] "OM292797.1" "OM292798.1" "OM295688.1" "OM295689.1" "OM295690.1"
## [151] "OM295691.1" "OM295692.1" "OM295693.1" "OM295694.1" "OM295695.1"
## [156] "OM295696.1" "OM295697.1" "OM295698.1" "OM295699.1" "OM321445.1"
## [161] "OM321446.1" "OM321447.1" "OM321448.1" "OM321449.1" "OM321450.1"
## [166] "OM321451.1" "OM321452.1" "OM321453.1" "OM321454.1" "OM321455.1"
## [171] "OM321460.1" "OM321461.1" "OM321462.1" "OM321463.1" "OM321464.1"
## [176] "OM321465.1" "OM321466.1" "OM321467.1" "OM321468.1" "OM321469.1"
## [181] "OM321470.1" "OM321471.1" "OM321472.1" "OM321473.1" "OM321474.1"
## [186] "OM321475.1" "OM327611.1" "OM327612.1" "OM327613.1" "OM327614.1"
## [191] "OM327615.1" "OM327616.1" "OM327617.1" "OM327618.1" "OM327619.1"
## [196] "OM327620.1" "OM327624.1" "OM327631.1" "PV918954.1" "PV918955.1"
## [201] "PV918956.1" "PV918957.1" "PV918958.1" "PV918959.1" "PV918962.1"
## [206] "PV918963.1" "PV918964.1" "PV918965.1" "PV918966.1" "PV918967.1"
## [211] "PV918968.1" "PV918969.1" "PV918970.1" "PV918971.1" "PV919004.1"
## [216] "PV919005.1" "PV919006.1" "PV919007.1" "PV919008.1" "PV919010.1"
## [221] "PV919011.1" "PV919012.1" "PV919013.1" "PV919014.1" "PV919015.1"
## [226] "PV919016.1" "PV919017.1" "PV919018.1" "PV919019.1" "PV919020.1"
## [231] "PV919021.1" "PV919022.1" "PV919023.1" "PV919024.1" "PV919038.1"
## [236] "PV919039.1" "PV919040.1" "PV919041.1" "PV919042.1" "PV919043.1"
## [241] "PV919044.1" "PV919045.1" "PV919046.1" "PV919047.1" "PV919048.1"
## [246] "PV919049.1" "PV919050.1" "PV919051.1" "PV919063.1" "PV919064.1"
## [251] "PV919065.1" "PV919135.1" "PV919136.1" "PV919137.1" "PV919138.1"
## [256] "PV919139.1" "PV919140.1" "PV919141.1" "PV919142.1" "PV919149.1"
## [261] "PV919150.1" "PV919151.1" "PV919152.1" "PV919461.1" "PV919462.1"
## [266] "PV919463.1" "PV919473.1" "PV919474.1" "PV919515.1" "PV919516.1"
## [271] "PV928216.1" "PV928217.1" "PV928218.1" "PV928219.1" "PV928220.1"
## [276] "PV928228.1" "PV928229.1" "PV928230.1" "PV928231.1" "PV928232.1"
## [281] "PV928233.1" "PV928234.1" "PV928261.1" "PV928262.1" "PV928263.1"
## [286] "PV928264.1" "PV928265.1" "PV928266.1" "PV928267.1" "PV928268.1"
## [291] "PV928269.1" "PV928270.1" "PV928271.1" "PV928272.1" "PV928273.1"
## [296] "PV928300.1" "PV928305.1" "PV928306.1" "PV928307.1" "PV928668.1"
## [301] "PV928669.1" "PV928743.1" "PV928744.1" "PV928745.1" "PV928944.1"
## [306] "PV928945.1" "PV928948.1" "PV928949.1" "PV928952.1" "PV928953.1"
## [311] "PV928955.1" "PV928996.1" "PV928998.1" "PV929010.1" "PV929014.1"
## [316] "PV929015.1" "PV929016.1" "PV929020.1" "PV929023.1" "PV929024.1"
## [321] "PV929025.1" "PV929026.1" "PV929027.1" "PV929048.1" "PV929049.1"
## [326] "PV929050.1" "PV929051.1" "PV929055.1" "PV929056.1" "PV929057.1"
## [331] "PV929058.1" "PV929059.1" "PV929060.1" "PV929061.1" "PV929062.1"
## [336] "PV929063.1" "PV929064.1" "PV929065.1"