Difference between revisions of "Mpetredi Week 3"
From LMU BioDB 2013
(Added some answers to individual journal) |
(added more answers to individual assignment) |
||
| Line 14: | Line 14: | ||
#cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | rev | sed "s/.../& /g" | sed -f genetic-code.sed | #cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | rev | sed "s/.../& /g" | sed -f genetic-code.sed | ||
| − | # | + | #cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | sed "s^.//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed |
| + | #cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | sed "s^..//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed | ||
| − | + | ==XMLPipeDB Match Practice== | |
| + | # java -jar xmlpipedb-match-1.1.1.jar "GO:000916." < 493.P_falciparum.xml | ||
| + | #* There were 2 unique matches | ||
| + | #* Each unique match appears twice in the first line and once in the second line | ||
Revision as of 04:44, 13 September 2013
Compliment of a Strand
cat infA-E.coli-K12.txt | sed "y/atcg/tagc/"
Reading Frames
Positive (Forward)
- cat infA-E.coli-K12.txt | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed
- cat infA-E.coli-K12.txt | sed "s/^.//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed
- cat infA-E.coli-K12.txt | sed "s/^..//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed
Negative (Reverse)
- cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | rev | sed "s/.../& /g" | sed -f genetic-code.sed
- cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | sed "s^.//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed
- cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | sed "s^..//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed
XMLPipeDB Match Practice
- java -jar xmlpipedb-match-1.1.1.jar "GO:000916." < 493.P_falciparum.xml
- There were 2 unique matches
- Each unique match appears twice in the first line and once in the second line
