Difference between revisions of "Emilysimso Week 3"
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| − | Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand. | + | ==Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand.== |
| − | Sequence used: gcattaggcaac | + | Sequence used: 5'-gcattaggcaac-3' |
* Used sed "y/atgc/tacg/" to perform complimentary base pairing | * Used sed "y/atgc/tacg/" to perform complimentary base pairing | ||
| − | Resulting sequence: cgtaatccgttg | + | Resulting sequence: 3'-cgtaatccgttg-5' |
| + | |||
| + | |||
| + | ==Write 6 sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence.== | ||
| + | Sequence used: 5'-gcattaggcaac-3' | ||
| + | * Used sed "y/t/u/" to change all t's to u's | ||
| + | Resulting sequence: 5'-gcauuaggcaac-3' | ||
| + | |||
| + | ===+1 Reading Frame: 5'-gca uua ggc aac-3'=== | ||
| + | * Used "sed "s/gca/A/g" to replace the first codon with A | ||
| + | Resulting sequence: 5'-AuuagAac-3' | ||
| + | * This is not the desired result | ||
| + | * Used "sed "s/^gca/A/g" to replace only the first codon with A | ||
| + | Resulting sequence: 5'-Auuaggcaac-3' | ||
| + | * Used "sed "s/uua/L/g" then sed "s/ggc/G/g" then sed "s/aac/N/g" to get the final result | ||
| + | +1 Reading Frame Amino Acids: ALGN | ||
| + | |||
| + | ===+2 Reading Frame: 5'-g cau uag gca ac-3'=== | ||
| + | * Used sed "s/^g/ /g" then sed "s/cau/H/g" then "s/uaggcaac/ stop/g" | ||
| + | Resulting sequence: H stop | ||
| + | |||
| + | ===+3 Reading Frame: 5'-gc auu agg caa c-3'=== | ||
| + | * Used sed "s/^gc/ /g" then sed "s/auu/I/g" then sed "s/agg/R/g" then sed "s/caa/Q/g" then sed "s/c$/ /g" | ||
| + | Resulting Sequence: IRQ | ||
Revision as of 03:05, 19 September 2015
Contents
- 1 Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand.
- 2 Write 6 sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence.
Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand.
Sequence used: 5'-gcattaggcaac-3'
- Used sed "y/atgc/tacg/" to perform complimentary base pairing
Resulting sequence: 3'-cgtaatccgttg-5'
Write 6 sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence.
Sequence used: 5'-gcattaggcaac-3'
- Used sed "y/t/u/" to change all t's to u's
Resulting sequence: 5'-gcauuaggcaac-3'
+1 Reading Frame: 5'-gca uua ggc aac-3'
- Used "sed "s/gca/A/g" to replace the first codon with A
Resulting sequence: 5'-AuuagAac-3'
- This is not the desired result
- Used "sed "s/^gca/A/g" to replace only the first codon with A
Resulting sequence: 5'-Auuaggcaac-3'
- Used "sed "s/uua/L/g" then sed "s/ggc/G/g" then sed "s/aac/N/g" to get the final result
+1 Reading Frame Amino Acids: ALGN
+2 Reading Frame: 5'-g cau uag gca ac-3'
- Used sed "s/^g/ /g" then sed "s/cau/H/g" then "s/uaggcaac/ stop/g"
Resulting sequence: H stop
+3 Reading Frame: 5'-gc auu agg caa c-3'
- Used sed "s/^gc/ /g" then sed "s/auu/I/g" then sed "s/agg/R/g" then sed "s/caa/Q/g" then sed "s/c$/ /g"
Resulting Sequence: IRQ
