HW2 - Introduction to Biocluster and Linux

2 minute read

Topic: Linux Basics

1. Download code from this page

   wget https://cluster.hpcc.ucr.edu/~tgirke/Linux.sh --no-check-certificate 
   

2. Download Halobacterium proteome and inspect it

   wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/archaea/Halobacterium_salinarum/representative/GCA_004799605.1_ASM479960v1/GCA_004799605.1_ASM479960v1_protein.faa.gz
   gunzip GCA_004799605.1_ASM479960v1_protein.faa.gz
   mv GCA_004799605.1_ASM479960v1_protein.faa halobacterium.faa
   less halobacterium.faa # press q to quit
   

3. How many protein sequences are stored in the downloaded file?

   grep '>' halobacterium.faa | wc
   grep '^>' halobacterium.faa --count
   

4. How many proteins contain the pattern WxHxxH or WxHxxHH?

   egrep 'W.H..H{1,2}' halobacterium.faa --count
   

5. Use less to find IDs for pattern matches or use awk

   awk --posix -v RS='>' '/W.H..(H){1,2}/ { print ">" $0;}' halobacterium.faa | less
   awk --posix -v RS='>' '/W.H..(H){1,2}/ { print ">" $0;}' halobacterium.faa | grep '^>' | cut -c 2- | cut -f 1 -d\ > myIDs
   

6. Create a BLASTable database with formatdb

   module load ncbi-blast
   makeblastdb -in halobacterium.faa -out halobacterium.faa -dbtype prot -hash_index -parse_seqids
   

7. Query BLASTable database by IDs stored in a file (e.g. myIDs)

   blastdbcmd -db halobacterium.faa -dbtype prot -entry_batch myIDs -get_dups -out myseq.fasta
   

8. Run BLAST search for sequences stored in myseq.fasta

   blastp -query myseq.fasta -db halobacterium.faa -outfmt 0 -evalue 1e-6 -out blastp.out
   blastp -query myseq.fasta -db halobacterium.faa -outfmt 6 -evalue 1e-6 -out blastp.tab
   

9. Return system time and host name

   date
   hostname
   

Additional exercise material in Linux Manual

Homework assignment

Perform above analysis on the protein sequences from E. coli. A right click on the link will allow you to copy the URL so that it can be used together with wget. Record result from final BLAST command (with outfmt 6) in text file.

Homework submission

Submit your homework to GEN242-2021 HW2 on GitHub Classroom by following these stepwise instructions:

1. Upload your script and name it hw2.sh.
2. Upload the unzipped faa file from step 1, name it ecoli.faa.
3. Upload IDs from step 5 in a file named myIDs.
4. Upload the final file generated with outfmt 6 from step 8, and name it ecoli.txt.

Due date

Most homeworks will be due one week after they are assigned. This one is due on Thu, April 8th at 6:00 PM.

Homework solution

See here.