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NameVersionResource
blast2.2.30Tusker
blast2.4.0Tusker
blast2.6.0Tusker
blast2.2.29Crane
blast2.2.30Crane
blast2.4.0Crane
blast2.6.0Crane

 

BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) is a local alignment tool that finds similarity between sequences. This tool compares nucleotide or protein sequences to sequence databases, and calculates significance of matches. Sometimes these input sequences are large and using the command-line BLAST is required.

The following pages, Create Local BLAST Database and Running BLAST Alignment describe how to run some of the most common BLAST executables as a single job under the SLURM scheduler on HCC.

 

Useful Information

In order to test the BLAST (blast/2.2) performance on Tusker, we aligned three nucleotide query datasets, small.fasta, medium.fasta and large.fasta, against the non-redundant nucleotide nt.fasta database from NCBI. Some statistics about the query datasets and the time and memory resources required for the alignment are shown on the table below:

 

total # of sequences

total # of bases

total size in MB

required time

required memory

# of used CPUs

small.fasta

41,715

35,581,740

37.627 MB

~ 2 hours

~ 23 GB

8

medium.fasta

110,478

147,543,113

149 MB

~ 4 hours

~ 24 GB

8

large.fasta

592,593

827,629,204

836 MB

~ 15 hours

~ 47 GB

8

 

 

 

 

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