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.

Quick Start

Generate only sequence alignments for input.fasta:

cyrus submit blast input.fasta --mode nopssm

Generate sequence alignments and PSSM for input.fasta:

cyrus submit blast input.fasta --mode pssm

Generate sequence alignments and patent information for input.fasta:

cyrus submit blast input.fasta --mode patent

Generate sequence alignments and return up to 1000 hits for input.fasta:

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 database
- pssm - run BLAST+ (psiblast) for sequence alignments and PSSM generation using NR database
- patent - 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

Outputs

Some outputs depend on the mode you choose to run.

Mode	Filename	Description
`nopssm`, `pssm`, `patent`	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)
`nopssm`, `pssm`, `patent`	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
`nopssm`, `pssm`, `patent`	full-query.fasta	FASTA file with complete sequences and descriptions from query hits
`pssm`	query.chk	PSSM checkpoint file generated by PSIBLAST
`pssm`	query.pssm	PSSM from PSIBLAST query in NCBI formatting
`patent`	query.patents	Textfile listing NCBI accession codes and patent descriptions for each query hit (ex. “ADA00576.1 Sequence 10 from patent US 7595057”)

References

NCBI Patent Database FAQs