Difference between revisions of "Kevinmcgee Week 3"
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Kevinmcgee (Talk | contribs) (Created week three page) |
Kevinmcgee (Talk | contribs) (Added XML match homework) |
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| + | ==Genetic Code By Computer== | ||
| − | [[Kevinmcgee | | + | ===Complementary Strand=== |
| − | [[ | + | |
| + | seq_file | sed "y/actg/tagc/" | ||
| + | |||
| + | ===Reading Frame Codes=== | ||
| + | +1 seq_file | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | +2 seq_file | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | +3 seq_file | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | -1 seq_file | sed "y/actg/tgac/" | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | -2 seq_file | sed "y/actg/tgac/" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | -3 seq_file | sed "y/actg/tgac/" | rev | 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 | ||
| + | :*First match occurred twice, second match occured once. | ||
| + | :* There appears to be multiple references to this in the doccument. It appears to be a specific alignment on a protein sequence of 493.P-Falciparum | ||
| + | #What Match command tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file? | ||
| + | :*2 Unique matches | ||
| + | :*First match occurred 8238 times, second match occurred 1 time. | ||
| + | :*When I typed in the command grep "\James.*\"", it told me that it was a persons name. By looking at the title and noticing the file is copyrighted, I believe that it is safe to assume that James K.D. is the name of an author of a scientific article. | ||
| + | #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. | ||
| + | :* Match brought back 830,101 matches | ||
| + | :* grep and wc gave me 502,401 lines, 502,401 words and 35671048 letters | ||
| + | :* It makes sense that grep and wc had less matches because they cannot account for multiple matches on the same line. | ||
| + | |||
| + | [[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 11:14, 12 September 2013 (PDT) | ||
| + | |||
| + | [[Category:Journal Entry]] | ||
Latest revision as of 18:40, 12 September 2013
Contents |
[edit] Genetic Code By Computer
[edit] Complementary Strand
seq_file | sed "y/actg/tagc/"
[edit] Reading Frame Codes
+1 seq_file | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed +2 seq_file | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed +3 seq_file | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed -1 seq_file | sed "y/actg/tgac/" | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed -2 seq_file | sed "y/actg/tgac/" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed -3 seq_file | sed "y/actg/tgac/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
[edit] XMLPipeDB Match Practice
- What Match command tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file?
- 2 unique matches
- First match occurred twice, second match occured once.
- There appears to be multiple references to this in the doccument. It appears to be a specific alignment on a protein sequence of 493.P-Falciparum
- What Match command tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file?
- 2 Unique matches
- First match occurred 8238 times, second match occurred 1 time.
- When I typed in the command grep "\James.*\"", it told me that it was a persons name. By looking at the title and noticing the file is copyrighted, I believe that it is safe to assume that James K.D. is the name of an author of a scientific article.
- 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.
- Match brought back 830,101 matches
- grep and wc gave me 502,401 lines, 502,401 words and 35671048 letters
- It makes sense that grep and wc had less matches because they cannot account for multiple matches on the same line.
Kevinmcgee (talk) 11:14, 12 September 2013 (PDT)
