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Table of Contents

Quick Start

Generate only sequence alignments for input.fasta:

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Code Block
cyrus submit blast input.fasta --mode nopssm --max-target-sequences 1000

--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). Note, there is a risk of diluting PSSM statistics if this maximum is set too high.

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”)

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