For the following exercise use the python file :download:`sv40 in fasta <_static/code/sv40.py>` which is a python file with the sequence of sv40 in fasta format
already embeded, and use python -i sv40.py to work.
| The il2_human contains 4 cysteins (C) in positions 9, 78, 125, 145. We want to generate the sequence of a mutatnt were the cysteins 78 and 125 are replaced by serins (S)
| write the pseudo code, before to propose an implementation:
take care of the string numbered vs sequence numbered:
| C in seq -> in string
| 9 -> 8
| 78 -> 77
| 125 -> 124
| 145 -> 144
| generate 3 slices from the il2_human
| head : from the begining and cut between the first cytein and the second
| body include the 2nd and 3rd cystein
| tail cut after the 3rd cystein until the end
| replace body cystein by serin
| make new sequence with head body_mutate tail
::
head = il2_human[:77]
body = il2_human[77:125]
tail = il2_human[126:]
body_mutate = body.replace('C', 'S')
il2_mutate = head + body_mutate + tail
Exercise
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# use again the sv40 sequence and compute the gc%
# generate a "micro" report like this 'the sv40 is 5243 bp lenght and have 40.80% gc'