ANSWERS to HOMEWORK 4

1. Answers to the 2nd questions:
   • The full path of your home directory is /home/YourtakLoginName. The command to get it is pwd.
   • If it's your first time logging in tak or hebrides, 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 /home/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 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_523822 > 1.fasta
     fastacmd -d SeqFileName -s NP_477425 > 2.fasta
     fastacmd -d SeqFileName -s NP_523453 > 3.fasta
     

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

     cat 1.fasta 2.fasta 3.fasta > my.fasta  
     

3. Answers to the 4th questions:
   The browser indicates that NM_007554 is not a full length cDNA. It misses exons at the 5'end.
   You can extract the promoter sequence by clicking on the alignment link of your full length cDNA in browser, clicking on the Genomic Sequence from assembly, change the Promoter/Upstream from 1000 to 2500 bases.
   There is alternative splicing for the gene. BC034053, BF538517 and ENSMUSG00000021835 don't have the 2nd exon.

4. Answers to the 5th 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.