blast_blastx

Tags: blast blastx alignment translation protein dna search fasta sample-scope

Search a protein database using a translated nucleotide query.

Uses BLASTX to translate nucleotide query sequences (FASTA) in all six reading frames and align them against a protein BLAST database. This is useful for identifying potential coding regions in unannotated DNA.

Inputs

record (
    meta: Record,
    blastdb: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
blastdb	Path	A compressed tarball containing the protein BLAST database

query: Path

Name	Type	Description
query	Path	FASTA file containing nucleotide query sequences

Outputs

record (
    meta: Record,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Tab-delimited translated nucleotide-to-protein alignment results (BLAST outfmt 6)
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

BLASTX Parameters

Parameter	Type	Default	Description
--blastx_query	string		A fasta file containing the query sequences to BLAST against the database
--blastx_outfmt	string	sseqid qseqid pident qlen slen length nident positive mismatch gapopen gaps qstart qend sstart send evalue bitscore	The columns to include with -outfmt 6
--blastx_opts	string		Additional options to pass to BLASTN
--blastx_qcov_hsp_perc	integer	50	Percent query coverage per hsp
--blastx_max_target_seqs	integer	2000	Maximum number of aligned sequences to keep

Used By

Subworkflows

• blastx - Translate nucleotide sequences and search protein database.

Workflows

• blastx - Search against protein BLAST databases using translated nucleotide queries.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• BLAST
  Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009)

Source

View source on GitHub

Version

BLAST_BLASTX:
    - blast: 2.17.0