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coolneng 2021-05-04 11:12:47 +02:00
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#+TITLE: locigenesis
#+AUTHOR: Amin Kasrou Aouam
#+DATE: 2021-03-10
* Sequence alignment
Our generated sequences contain the full VJ region, but we are only interested in the CDR3 (Complementarity-determining region). We will proceed by delimiting CDR3, using the known sequences of V and J.
#+begin_src R :results value silent
v_segments <- readRDS("data/v_segments.rds")
j_segments <- readRDS("data/j_segments_phe.rds")
#+end_src
#+begin_src R
print(v_segments)
print(j_segments)
#+end_src
#+RESULTS:
#+begin_example
A DNAStringSet instance of length 147
width seq names
[1] 326 GATACTGGAATTACCCAGACAC...ATCTCTGCACCAGCAGCCAAGA TRBV1*01_P
[2] 326 GATGCTGAAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-1*01_F
[3] 326 GATGCTGAAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-1*02_F
[4] 326 GATGCTGGAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-2*01_F
[5] 326 GATGCTGGAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-2*02_F
... ... ...
[143] 324 GATACTGGAGTCTCCCAGAACC...GTATCTCTGTGCCAGCACGTTG TRBV7-9*06_(F)
[144] 323 .........................TGTATCTCTGTGCCAGCAGCAG TRBV7-9*07_(F)
[145] 325 GATTCTGGAGTCACACAAACCC...TATTTCTGTGCCAGCAGCGTAG TRBV9*01_F
[146] 325 GATTCTGGAGTCACACAAACCC...TATTTCTGTGCCAGCAGCGTAG TRBV9*02_F
[147] 321 GATTCTGGAGTCACACAAACCC...TTTGTATTTCTGTGCCAGCAGC TRBV9*03_(F)
A DNAStringSet instance of length 16
width seq names
[1] 32 TGGGCGTCTGGGCGGAGGACTCCTGGTTCTGG TRBJ2-2P*01_ORF
[2] 31 TTTGGAGAGGGAAGTTGGCTCACTGTTGTAG TRBJ1-3*01_F
[3] 31 TTTGGTGATGGGACTCGACTCTCCATCCTAG TRBJ1-5*01_F
[4] 31 TTTGGCAGTGGAACCCAGCTCTCTGTCTTGG TRBJ1-4*01_F
[5] 31 TTCGGTTCGGGGACCAGGTTAACCGTTGTAG TRBJ1-2*01_F
... ... ...
[12] 31 TTTGGCCCAGGCACCCGGCTGACAGTGCTCG TRBJ2-3*01_F
[13] 31 TTCGGGCCAGGCACGCGGCTCCTGGTGCTCG TRBJ2-5*01_F
[14] 31 TTCGGGCCAGGGACACGGCTCACCGTGCTAG TRBJ2-1*01_F
[15] 31 TTCGGGCCGGGCACCAGGCTCACGGTCACAG TRBJ2-7*01_F
[16] 31 GTCGGGCCGGGCACCAGGCTCACGGTCACAG TRBJ2-7*02_ORF
#+end_example