47 lines
2.2 KiB
Org Mode
47 lines
2.2 KiB
Org Mode
#+TITLE: locigenesis
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#+AUTHOR: Amin Kasrou Aouam
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#+DATE: 2021-03-10
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* Sequence alignment
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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.
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#+begin_src R :results value silent
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v_segments <- readRDS("data/v_segments.rds")
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j_segments <- readRDS("data/j_segments_phe.rds")
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#+end_src
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#+begin_src R
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print(v_segments)
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print(j_segments)
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#+end_src
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#+RESULTS:
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#+begin_example
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A DNAStringSet instance of length 147
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width seq names
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[1] 326 GATACTGGAATTACCCAGACAC...ATCTCTGCACCAGCAGCCAAGA TRBV1*01_P
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[2] 326 GATGCTGAAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-1*01_F
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[3] 326 GATGCTGAAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-1*02_F
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[4] 326 GATGCTGGAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-2*01_F
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[5] 326 GATGCTGGAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-2*02_F
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... ... ...
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[143] 324 GATACTGGAGTCTCCCAGAACC...GTATCTCTGTGCCAGCACGTTG TRBV7-9*06_(F)
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[144] 323 .........................TGTATCTCTGTGCCAGCAGCAG TRBV7-9*07_(F)
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[145] 325 GATTCTGGAGTCACACAAACCC...TATTTCTGTGCCAGCAGCGTAG TRBV9*01_F
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[146] 325 GATTCTGGAGTCACACAAACCC...TATTTCTGTGCCAGCAGCGTAG TRBV9*02_F
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[147] 321 GATTCTGGAGTCACACAAACCC...TTTGTATTTCTGTGCCAGCAGC TRBV9*03_(F)
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A DNAStringSet instance of length 16
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width seq names
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[1] 32 TGGGCGTCTGGGCGGAGGACTCCTGGTTCTGG TRBJ2-2P*01_ORF
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[2] 31 TTTGGAGAGGGAAGTTGGCTCACTGTTGTAG TRBJ1-3*01_F
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[3] 31 TTTGGTGATGGGACTCGACTCTCCATCCTAG TRBJ1-5*01_F
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[4] 31 TTTGGCAGTGGAACCCAGCTCTCTGTCTTGG TRBJ1-4*01_F
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[5] 31 TTCGGTTCGGGGACCAGGTTAACCGTTGTAG TRBJ1-2*01_F
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... ... ...
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[12] 31 TTTGGCCCAGGCACCCGGCTGACAGTGCTCG TRBJ2-3*01_F
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[13] 31 TTCGGGCCAGGCACGCGGCTCCTGGTGCTCG TRBJ2-5*01_F
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[14] 31 TTCGGGCCAGGGACACGGCTCACCGTGCTAG TRBJ2-1*01_F
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[15] 31 TTCGGGCCGGGCACCAGGCTCACGGTCACAG TRBJ2-7*01_F
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[16] 31 GTCGGGCCGGGCACCAGGCTCACGGTCACAG TRBJ2-7*02_ORF
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#+end_example
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