ANSWERS to HOMEWORK 4

1. Answers to the 2nd questions:
   • The full path of your home directory is /usr/people/YourFladdaLoginName. The command to get it is pwd.
   • If it's your first time logging in fladda, you wouldn't find any file in your home directory with the command ls.
   • You can find the hidden files with the command ls -a.
2. Answers to the 3rd questions:
   • To copy the blast input file BlastIN to your home directory, you could type cp /usr/people/yuan/wi_homework/hw4/BlastIN PathOfYourHomeDirectory. If you are currently at your home directory, you could use . for PathOfYourHomeDirectory. Otherwise, you could use ~ for PathOfYourHomeDirectory.
   • The command line for doing the blast search is blastall -p blastp -e 0.01 -i BlastIN -d SeqFileName -o 2seqs.blast.txt and blastall -p blastp -e 0.01 -T T -i BlastIN -d SeqFileName -o 2seqs.blast.html. In the 2seqs.blast.html, the target proteins were linked to protein entries in entrez. So, you could look at the descriptions of target proteins. The first query, drosophila odorant receptor 98a, was similar to all the fly odorant receptor proteins in this database. The second query, the mouse olfactory receptor 71, was similar to olfactory receptor in both human and mouse.
   • The command to retrieve each protein sequence and save them in individual file (for example, file names ending with .fasta):

     fastacmd -d SeqFileName -s NP_524536.1 > 1st.fasta
     fastacmd -d SeqFileName -s NP_523624.1 > 2nd.fasta
     fastacmd -d SeqFileName -s NP_523822.1 > 3rd.fasta
     fastacmd -d SeqFileName -s NP_477425.1 > 4th.fasta
     fastacmd -d SeqFileName -s NP_523453.1 > 5th.fasta
     

     The command line to combine the above 5 files into one file, and called the combined file as my.fasta:

     cat 1st.fasta 2nd.fasta 3rd.fasta 4th.fasta 5th.fasta >my.fasta  
     

   • In order to get the conserved regions with fuzzpro, you need to input your file (Ex. my.fasta), the pattern TIFVQF, mismatch number 1 and output filename. Then, you can see the conserved regions in the output file with the 'more' command. The result is:

                  gi   256 TIFVQF
                  gi   241 TIFTQF
                  gi   269 TIFVQF
                  gi   268 TIFVQF
                  gi   268 TIFVQF
     

3. Answers to the 4th questions:
   The command line for making the bioinfo_course directory is mkdir bioinfo_course. Then, you could do cd bioinfo_course to get into the bioinfo_course directory. Type the command mkdir homework_4 to make the homework_4 directory inside bioinfo_course directory. You could type the command mv ~/* homework_4/ to move all the files from your home directory to homework_4 directory.