Difference between revisions of "Gleis Week 3"
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==XMLPIPEDB MATCH== | ==XMLPIPEDB MATCH== | ||
| − | + | 1. What Match command tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file? | |
| − | : | + | :* Two unique matches |
| − | : | + | :* First unique match occurred twice. Second match occurred once |
| + | :* GO:000916 possibly represents a sequence identification number for a portion of a protein sequence. | ||
| + | |||
| + | 2. What Match command tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file? | ||
| + | :* Two unique matches | ||
| + | :* The first unique match occurred 8283 times and the second unique match occurred once. | ||
| + | :* \"James.*\" likely refers to the last name of an author in a journal article. | ||
| + | |||
| + | 3. 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. | ||
| + | :*830101 | ||
| + | :*502410 | ||
| + | :*The answers make sense because grep wc will only count the occurrence of ATG once per line even if ATG occurs more than once. | ||
| + | |||
| + | ==The Genetic Code, By Computer== | ||
| + | ===Complement of a Strand=== | ||
| + | cat sequence_file | sed "y/atgc/tacg/" | ||
| + | ===Reading Frames=== | ||
| + | +1 cat sequence_file | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | |||
| + | +2 cat sequence_file | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | |||
| + | +3 cat sequence_file | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | |||
| + | -1 cat sequence_file | sed "y/atgc/tacg/" | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | |||
| + | -2 cat sequence_file | sed "y/atgc/tacg/" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | |||
| + | -3 cat sequence_file | sed "y/atgc/tacg/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | |||
| + | [[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 22:18, 16 September 2013 (PDT) | ||
| + | |||
| + | [[Category:Journal Entry]] | ||
Latest revision as of 05:20, 17 September 2013
Contents |
[edit] XMLPIPEDB MATCH
1. What Match command tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file?
- Two unique matches
- First unique match occurred twice. Second match occurred once
- GO:000916 possibly represents a sequence identification number for a portion of a protein sequence.
2. What Match command tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file?
- Two unique matches
- The first unique match occurred 8283 times and the second unique match occurred once.
- \"James.*\" likely refers to the last name of an author in a journal article.
3. 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.
- 830101
- 502410
- The answers make sense because grep wc will only count the occurrence of ATG once per line even if ATG occurs more than once.
[edit] The Genetic Code, By Computer
[edit] Complement of a Strand
cat sequence_file | sed "y/atgc/tacg/"
[edit] Reading Frames
+1 cat sequence_file | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
+2 cat sequence_file | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
+3 cat sequence_file | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
-1 cat sequence_file | sed "y/atgc/tacg/" | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
-2 cat sequence_file | sed "y/atgc/tacg/" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
-3 cat sequence_file | sed "y/atgc/tacg/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
