Difference between revisions of "Emilysimso Week 3"
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* 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$/ /g" | * Used sed "s/^gc/ /g" then sed "s/auu/I/g" then sed "s/agg/R/g" then sed "s/caa/Q/g" then sed "s/c$/ /g" | ||
+3 Reading Frame Amino Acids: IRQ | +3 Reading Frame Amino Acids: IRQ | ||
| + | |||
| + | ===-1 Reading Frame: 5'-guu gcc uaa ugc-3' | ||
| + | * Used see "y/t/u/" to change t's to u's from complementary strand (3'-cgtaatccgttg-5' to 3'-cguaauccguug-5') | ||
| + | * Used echo "cguaauccguug" | rev" to reverse the strand | ||
| + | Resulting Stand: 5'-guugccuaaugc-3' | ||
| + | * Used sed "s/guu/V/g" then sed "s/gcc/A/g" then "s/uaa/ stop/g" then sed "s/ugc/ /g" | ||
| + | -1 Reading Frame Amino Acids: VA stop | ||
| + | |||
| + | ===-2 Reading Frame: 5'-g uug ccu aau gc-3'=== | ||
| + | * Used sed "s/^g/ /g" then sed "s/uug/L/g" then "s/ccu/P/g" then "s/aau/N/g" then sed "s/gc/ /g" | ||
| + | -2 Reading Frame Amino Acids: LPN | ||
| + | |||
| + | ===-3 Reading Frame: 5'-gu ugc cua aug c-3'=== | ||
| + | * Used sed "s/^gu/ /g" then sed "s/ugc/C/g" sed "s/cua/L/g" sed "s/aug/M/g" then sed "s/c/ /g" | ||
| + | -3 Reading Frame Amino Acids: CLM | ||
Revision as of 17:46, 20 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"
+2 Reading Frame Amino Acids: 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"
+3 Reading Frame Amino Acids: IRQ
===-1 Reading Frame: 5'-guu gcc uaa ugc-3'
- Used see "y/t/u/" to change t's to u's from complementary strand (3'-cgtaatccgttg-5' to 3'-cguaauccguug-5')
- Used echo "cguaauccguug" | rev" to reverse the strand
Resulting Stand: 5'-guugccuaaugc-3'
- Used sed "s/guu/V/g" then sed "s/gcc/A/g" then "s/uaa/ stop/g" then sed "s/ugc/ /g"
-1 Reading Frame Amino Acids: VA stop
-2 Reading Frame: 5'-g uug ccu aau gc-3'
- Used sed "s/^g/ /g" then sed "s/uug/L/g" then "s/ccu/P/g" then "s/aau/N/g" then sed "s/gc/ /g"
-2 Reading Frame Amino Acids: LPN
-3 Reading Frame: 5'-gu ugc cua aug c-3'
- Used sed "s/^gu/ /g" then sed "s/ugc/C/g" sed "s/cua/L/g" sed "s/aug/M/g" then sed "s/c/ /g"
-3 Reading Frame Amino Acids: CLM
