Topic: Linux Basics

  1. Download code from this page 
     wget http://biocluster.ucr.edu/~tgirke/Linux.sh
  2. Download Halobacterium proteome and inspect it 
     wget ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/archaea/Halobacterium_salinarum/representative/GCA_000006805.1_ASM680v1/GCA_000006805.1_ASM680v1_protein.faa.gz
 gunzip GCA_000006805.1_ASM680v1_protein.faa.gz
 mv GCA_000006805.1_ASM680v1_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

Additional exercise material in Linux Manual

Homework assignment

Perform above analysis on the following Escherichia coli strain: ftp://ftp.ncbi.nih.gov/genomes/genbank/bacteria/Escherichia_coli/latest_assembly_versions/GCA_000461395.1_Esch_coli_UMEA_3592-1_V1/GCA_000461395.1_Esch_coli_UMEA_3592-1_V1_protein.faa.gz. Record result from final BLAST command (with outfmt 6) in text file.

Homework submission

Upload result file to your private course GitHub repository under Homework/HW2/HW2.txt.

Due date

Most homeworks will be due one week after they are assigned. This one is due on Thu, April 12th at 6:00 PM.