Difference between revisions of "Vkuehn Week 3"
From LMU BioDB 2013
(Added reading frames) |
(reading frames finished) |
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===Complement of a Strand=== | ===Complement of a Strand=== | ||
cat sequence_file | grep "aggta" prokaryote.txt | sed "s/aggta/tccat/g" prokaryote.txt | cat sequence_file | grep "aggta" prokaryote.txt | sed "s/aggta/tccat/g" prokaryote.txt | ||
| − | ===Reading Frames=== | + | ===Reading Frames:=== |
+1 Reading Frame: | +1 Reading Frame: | ||
cat prokaryote.txt | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | cat prokaryote.txt | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| Line 11: | Line 11: | ||
===Reverse Reading Frames:=== | ===Reverse Reading Frames:=== | ||
-1 Reading Frame: | -1 Reading Frame: | ||
| − | + | rev prokaryote.txt | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | |
-2 Reading Frame: | -2 Reading Frame: | ||
| + | rev prokaryote.txt | sed "s/^./ /g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | -3 REading Frame: | ||
| + | rev prokaryote.txt | sed "s/^../ /g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| − | + | ===XMLPipeDB Match Practice:=== | |
| + | '''What Match command tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file?''' | ||
| + | * 2 unique matches | ||
| + | * One match appears once, and the other appears twice. | ||
| + | * I think this represents some kind of a protein marker or specific sequence. | ||
| + | '''What Match command tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file?''' | ||
| + | * dfajsdfao | ||
| + | *dsfasdf | ||
| + | * This information represents the authors who found certain proteins gene sequences. | ||
| + | '''Use Match to count the occurrences of the pattern ATG in the hs_ref_GRCh37_chr19.fa file (this may take a while). Then, use grep and wc to do the same thing.''' | ||
[[user: Vkuehn|Viktoria Kuehn]] | [[user: Vkuehn|Viktoria Kuehn]] | ||
Revision as of 18:42, 15 September 2013
Contents |
Individual Journal Assignment Week 3
Complement of a Strand
cat sequence_file | grep "aggta" prokaryote.txt | sed "s/aggta/tccat/g" prokaryote.txt
Reading Frames:
+1 Reading Frame:
cat prokaryote.txt | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
+2 Reading Frame:
cat prokaryote.txt | sed "s/^./ /g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
+3 Reading Frame:
cat prokaryote.txt | sed "s/^../ /g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
Reverse Reading Frames:
-1 Reading Frame:
rev prokaryote.txt | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
-2 Reading Frame:
rev prokaryote.txt | sed "s/^./ /g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
-3 REading Frame:
rev prokaryote.txt | sed "s/^../ /g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
XMLPipeDB Match Practice:
What Match command tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file?
- 2 unique matches
- One match appears once, and the other appears twice.
- I think this represents some kind of a protein marker or specific sequence.
What Match command tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file?
- dfajsdfao
- dsfasdf
- This information represents the authors who found certain proteins gene sequences.
Use Match to count the occurrences of the pattern ATG in the hs_ref_GRCh37_chr19.fa file (this may take a while). Then, use grep and wc to do the same thing.
