Ajvree Week 3
From LMU BioDB 2013
Week 3 Individual Assignment
Notes:
Shortcuts-
- cd to change directories, ls to view content
- up and down arrows to view command history, or type history, !number to redo that command
- CTRL R for reverse search- type in part of search, will recall past commands
- tab to fill in file name
- grep- text finder - looks for pattern: "ACTG" filename
- A followed by T with multiple things in between:
- . = "wildcard" "A......T"
- indicate beginning of line: ^ "^A......T"
- end of line: $ "A......T$"
- use previous command | wc to find word count for previously used file
- command|command
- wc- word count
- enter lines, then CTRL D
- lines, # words, #characters
XMLPipeDB Match Practice In-Class
Reading Frames
Write 6 sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence. In other words, fill in the question marks:
XMLPipeDB Match Practice
For your convenience, the XMLPipeDB Match Utility (xmlpipedb-match-1.1.1.jar) has been installed in the ~dondi/xmlpipedb/data directory alongside the other practice files. Use this utility to answer the following questions:
What Match command tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file?
How many unique matches are there?
How many times does each unique match appear?
What information do you think the pattern GO:000916. represents?
What Match command tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file?
How many unique matches are there?
How many times does each unique match appear?
What information do you think the pattern \"James.*\" represents?
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.
What answer does Match give you?
What answer does grep/wc give you?
Do the answers make sense? Explain your response.
