Prefilter BLAST

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Prefilter BLAST is a novel parallel prefiltering model written for NVidia GPU. Although it could be used with other algorithms, it has been specially developed and optimized for NCBI BLAST.

Features

Protein Filtering

• Stable version

Nucleotide Filtering

• Working in progress (alpha development version)

Metagenome

• Working in progress (alpha development version)

Requirements

Prefilter BLAST has been developed for NVidia GPU and its programming language CUDA. For that reason, CUDA and its dependecies must be installed. For further information, go to NVidia Developer Portal

Dependencies

• CUDA Runtime & Developer Toolkit (tested with CUDA 2.0)
• GCC compiler and development dependencies (glibc-dev)

Parameters

• -p: NCBI BLAST type (blastp for proteins, blastn for nucleotides and blastx for metagenomes).
• -d: Database file (i.e. non-redundant NR)
• -i: Query file (i.e. AMA protein family)
• -b: Filter mode (1 for different alignments, 2 for similar alignments; default 1)
• -o: Output FASTA file
• -f: Prefilter BLAST similarity threshold (default 0.5)
• -t: NCBI BLAST threshold (default 11)
• -c: GPU card number (specially for multi-GPU cards; default 0)
• -m: NCBI BLAST substitution matrix (i.e. BLOSUM62)
• -w: NCBI BLAST word size (3 for proteins and 11 for nucleotides)

Compilation

make

Execution

naudit_filter -p blastp -d db/nr.fasta.fdb -i db/Amaaa.fasta -b 2 -o salida -a 6 -t 0.7

Contribute

If you have any idea for an improvement or found a bug do not hesitate to open an issue.

License

Prefilter BLAST is distributed under MIT License.