The BLAST tools API runs standalone BLAST+ executables with v5 NCBI databases for design related queries. Three modes are available: nopssm, pssm, and patent for running standard BLAST sequence alignments and patent queries respectively. The nopssm and pssm modes run standard BLAST+ against the NR database; use the latter if you wish to generate a PSSM for your query. The patent mode runs BLAST+ against the curated NCBI patent protein sequence database (pataa) that is generated in partnership with the USPTO and will return specific patent sequence hits along with the standard alignments. See the blast-tools repository for a more customizable setup using Docker.
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Quick Start
Generate only sequence alignments for input.fasta:
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cyrus submit blast input.fasta --mode nopssm --max-target-sequences 1000 |
Inputs
FASTA file containing query sequence of interest.
Options
--fasta-file: Input FASTA file with query sequence--mode:nopssm- run BLAST+ (blastp) for sequence alignments using NR databasepssm- run BLAST+ (psiblast) for sequence alignments and PSSM generation using NR databasepatent- run BLAST+ (blastp) for sequence alignments and patent hits using PATAA database
--max-target-sequences: sets the maximum number of sequences that can be returned for a query (, default = 500). Note, there is a risk of diluting PSSM statistics if this maximum is set too high.
Outputs
Some outputs depend on the mode you choose to run.
Mode | Filename | Description |
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| query.out | BLASTP or PSIBLAST query alignments (Note: formatting differs between BLASTP and PSIBLAST - PSIBLAST is set to run 4 iterative rounds and data from each round is logged to this file) |
| query.entries | Accession IDs of query hits are parsed from query.out file for gathering the full sequences and descriptions for the full-query.fasta file |
| full-query.fasta | FASTA file with complete sequences and descriptions from query hits |
| query.chk | PSSM checkpoint file generated by PSIBLAST |
| query.pssm | PSSM from PSIBLAST query in NCBI formatting |
| query.patents | Textfile listing NCBI accession codes and patent descriptions for each query hit (ex. “ADA00576.1 Sequence 10 from patent US 7595057”) |
Workflow
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