Difference between revisions of "Laurmagee: Week 3"
From LMU BioDB 2013
(Added Codes) |
(Almost done with reading frames!) |
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#*cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed | #*cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed | ||
#Second Reading Frame (+2) | #Second Reading Frame (+2) | ||
| − | #*cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed | + | #*cat sequence_file | sed "s/^.//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed |
#Third Reading Frame (+3) | #Third Reading Frame (+3) | ||
| − | #*cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed | + | #*cat sequence_file | sed "s/^..//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed |
#Fourth Reading Frame (-1) | #Fourth Reading Frame (-1) | ||
| − | #*cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed | + | #*cat sequence_file | sed "y/atgc/tacg/" |rev| sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed |
#Fifth Reading Frame (-2) | #Fifth Reading Frame (-2) | ||
| − | #*cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed | + | #*cat sequence_file | sed "s/^.//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed |
#Sixth Reading Frame (-3) | #Sixth Reading Frame (-3) | ||
| − | #*cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed | + | #*cat sequence_file | sed "s/^..//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed |
==XMLPipeDB Match Practice== | ==XMLPipeDB Match Practice== | ||
Revision as of 18:24, 12 September 2013
Complement of a Strand
- The appropriate processing commands are the following: cat sequence_file | sed "y/atgc/tacg/"
- This will turn a nucleotide sequence, "agcggtatac", into "tcgccatatg", it's compliment.
Reading Frames
- First Reading Frame (+1)
- cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
- Second Reading Frame (+2)
- cat sequence_file | sed "s/^.//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
- Third Reading Frame (+3)
- cat sequence_file | sed "s/^..//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
- Fourth Reading Frame (-1)
- cat sequence_file | sed "y/atgc/tacg/" |rev| sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
- Fifth Reading Frame (-2)
- cat sequence_file | sed "s/^.//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
- Sixth Reading Frame (-3)
- cat sequence_file | sed "s/^..//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
