Running and Verifying BLAST

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Use an SFTP tool to upload the test case to the /path/to/CASE directory.
3. Run the following commands to decompress and rename Swissprot Proteins data:

   cd /path/to/CASE
   gzip -d swissprot.gz
   mv swissprot swissprot.fa

4. Run the following commands to save all files to the data directory:

   mkdir data
   mv swissprot.fa data/
   mv protein_query.fasta data/

5. Run the following commands to compile the test case data.

   export PATH=$BLAST_TOP/c++/ReleaseMT/bin:$PATH
   makeblastdb -in data/swissprot.fa -dbtype prot

   After the commands are executed, the following four files are generated in the data directory. You can run the ls command to view the files.

   • swissprot.fa
   • swissprot.fa.phr
   • swissprot.fa.pin
   • swissprot.fa.psq
6. Run the following command to run the test:

   { time blastp -query data/protein_query.fasta -db data/swissprot.fa ; } 2>&1 |tee output_protein_alignments.txt

   View the real value in the last time command output in the log. The value indicates x minutes y seconds. The lower the value is, the better the performance is.

   Figure 1 shows the command output.

   Figure 1 Test example