BLAST API

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.

Command Line Interface

Examples

Generate only sequence alignments for input.fasta:

lev engine submit blast input.fasta \
    --mode nopssm

Generate sequence alignments and PSSM for input.fasta:

lev engine submit blast input.fasta \
    --mode pssm

Generate sequence alignments and patent information for input.fasta:

lev engine submit blast input.fasta \
    --mode patent

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

lev engine submit blast input.fasta \
    --mode nopssm \
    --max-target-sequences 1000

Flags

  • --fasta-file (str) (Required)
    • Input FASTA file with query sequence
  • --max-target-sequences (int) (Default: 500)
    • Sets the maximum number of sequences that can be returned for a query
  • --mode (str) (Required)
    • Sets the mode for the BLAST run.
    • Options:
      • 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

Python Interface

Examples

from engine import EngineClient

client = EngineClient()
client.authorize()

# Generate sequence alignments only
result = submit_blast(
    fasta_path="input.fasta",
    mode="nopssm"
)

# Generate sequence alignments and PSSM
result = submit_blast(
    fasta_path="input.fasta",
    mode="pssm"
)

# Generate sequence alignments with patent information
result = submit_blast(
    fasta_path="input.fasta",
    mode="patent"
)

# Generate alignments with custom number of hits
result = submit_blast(
    fasta_path="input.fasta",
    mode="nopssm",
    max_target_sequences=1000
)

Flags

  • fasta_path (str) (Required)
    • FASTA file containing query sequence of interest.
  • max_target_sequences (int) (Default: 500)
    • Sets the maximum number of sequences that can be returned for a query
  • mode (str) (Required)
    • Sets the mode for the BLAST run.
    • Options:
      • 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

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

Updated: