HDelgadi Week 3

Complementary Strand

cat seq_file | sed "y/tagc/atcg/"

6 Different Reading Frames

+1 Reading Frame

1. cat sequence_file | sed "s/.../& /g" | sed "s/t/u/g" | sed genetic-code.sed

+2 Reading Frame

1. cat sequence_file | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed genetic-code.sed

+3 Reading Frame

1. cat sequence_file | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed genetic-code.sed

-1 Reading Frame

1. rev sequence_file | sed "y/atgc/tacg/" | sed "s/.../& /g" | sed "s/t/u/g" | sed genetic-code.sed

-2 Reading Frame

1. rev sequence_file | sed "y/atgc/tacg/" | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed genetic-code.sed

-3 Reading Frame

1. rev sequence_file | sed "y/atgc/tacg/" | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed genetic-code.sed

XMLPipeDB Match Practice

• What Match command tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file?

The command: java -jar xmlpipedb-match-1.1.1.jar "GO:000916." <493.P_falciparum.xml.

• How many unique matches are there?

There are two unique matches.

• How many times does each unique match appear?

go:0009165 appears twice and go:0009168 appears once.

• What information do you think the pattern GO:000916. represents?

This pattern might represent the proteins in the organism Falciparum.

• What Match command tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file?

The command: java -jar xmlpipedb-match-1.1.1.jar "\"James.*\"" < 493.P_falciparum.xml.

• How many unique matches are there?

There are two unique matches.

• How many times does each unique match appear?

"james k.d." appears 8238 times and "james a.a." appears just once.

• What information do you think the pattern \"James.*\" represents?

This pattern can represent the different labeled proteins.

• What answer does Match give you?

• What answer does grep/wc give you?

• Do the answers make sense? Explain your response.