BLAST

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BLAST (basic local alignment search tool) is a software package for aligning nucleotide or amino acid sequences, and its primary use is to search databases for sequences that are similar to a given candidate sequence.

Contents

Availability

Resource Centre Description
Beda C3SE throughput cluster resource
Kalkyl UPPMAX cluster resource of about 21 TFLOPS
Kappa NSC throughput cluster resource of 26 TFLOPS
Matter NSC cluster resource of 37 TFLOPS dedicated to materials science
Triolith NSC Capability cluster with 338 TFLOPS peak and 1:2 Infiniband fat-tree

Versions

There are two BLAST versions that are in current widespread use; the legacy NCBI BLAST and the new rewrite BLAST+.

BLAST+ was written to improve performance and maintainability, and to facilitate introduction of new features. It is similiar in most respects and has been made almost completely backwards compatible, by way of a wrapper script called ./legacy_blast.pl. New projects are encouraged to use BLAST+ if at all possible.


Computational considerations

Work locally

Many of the features in BLAST require access to database flatfiles, and standard practice when running a compute cluster is to copy all necessary files to a node local directory before any work is done with them. This behaviour is highly encouraged on most resources, since multiple simultaneous accesses to the same large files on a shared disk is likely to cause problems for all computations currently running on the resource, and not only for the owner of the badly behaving jobs. For this reason, most SNIC resources have amenities in place to aid you in running your BLAST jobs in an optimal manner (for example prepare_db and $BLASTDB, described for example here).

Use all your processors

BLAST uses only one processor core by default, but you increase this number using the -a command line option (-num_threads for BLAST+), which can often provide a significant increase in speed. If you are using a preinstalled BLAST version on a SNIC resource, the recommended number of cores to use is given by the $BLAST_NUM_CPUS environment variable (e.g. used like blastall -a $BLAST_NUM_CPUS ... ). However, in some situations you may want to consider decreasing this number, particularly if your searches generate a large enough number of hits to deplete RAM, causing the OS to start swapping data and results to disk, which will near slow your job to a stop (see below).

Do not run out of memory

If possible, you should ensure that you have enough RAM to hold the database as well as the results and still have some headroom. This ensures that BLAST will not need to read data from disk unnecessarily, which otherwise would cause significant slowdown. This can be done for example by:

License

License: Free.

Experts

No experts have currently registered expertise on this specific subject. List of registered field experts:
Field AE FTE General activities
Henric Zazzi (PDC) PDC Bioinformatics 100100 Bioinformatics Application support
Joel Hedlund (NSC) NSC Bioinformatics 00
Martin Dahlö (UPPMAX) UPPMAX Bioinformatics 1010 Bioinformatic support
Sebastian DiLorenzo (UPPMAX) UPPMAX Bioinformatics 5050 National bioinformatic support, NGS tumor data

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