FASTA

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FASTA is a software package for aligning nucleotide or amino acid sequences. Its primary use is to search databases for sequences that are similar to a given candidate sequence.

Contents

Computational considerations

Work locally

Many of the features in FASTA 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.

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 FASTA will not need to read data from disk unnecessarily, which otherwise would cause significant slowdown. This can be done for example by:

Availability

Resource Centre Description
Triolith NSC Capability cluster with 338 TFLOPS peak and 1:2 Infiniband fat-tree

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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