Remote NCBI BLAST and CDD Requests

Task Name: remote-request

Performs remote requests to the NCBI and saves the results as annotations.

Parameters:

in — A semicolon-separated list of input files. A file can be of any format containing sequences or alignments. [String, Required]

db — Database to search in. [String, Optional, Default: “ncbi-blastn”]

The following databases are available:

• “ncbi-blastn” for nucleotide sequences
• “ncbi-cdd” for amino acid sequences
• “ncbi-blastp” for amino acid sequences

out — Output Genbank file. [String, Required]

eval — Specifies the statistical significance threshold for reporting matches against database sequences. [Number, Optional, Default: 10]

hits — Maximum number of hits that will be shown. [Number, Optional, Default: 10]

name — Name of the result annotations. If not set, the name will be specified with the “cdd” result or the “blast” result. [String, Optional, Default: “cdd” or “blast”]

short — Optimizes search for short sequences. [Boolean, Optional, Default: false]

blast-output — Path to the file with the NCBI-BLAST output (only for the “ncbi-blastp” and “ncbi-blastn” databases). [Boolean, Optional, Default: the file is not saved]

Example:

ugene remote-request –in=seq.fa –db=ncbi-blastp –out=res.gb