NCBI Blast - Online

Introduction

NCBI offers a public service, QBlast, that searches molecular sequence databases with the Blast algorithm. Its main advantages are its versatility and that no database maintenance is required. Performance depends on the availability of the NCBI servers.

NCBI Blast - Online is one of the ways to run a Blast search in OmicsBox. See Blast Search for the overall Blast workflow and where to launch it.

Run

Select NCBI Blast on the first page of the Blast wizard. The Blast Configuration page provides the following parameters:

• Email. An e-mail address to associate to the analysis. Required by the NCBI Blast web service.

• Blast Program. The Blast algorithm, chosen according to the type of the query sequences and of the database. The main programs are:

  • blastp: protein query against a protein database.
  • blastx: nucleotide query, translated in all six reading frames, against a protein database. Used to find the potential protein products of an unknown nucleotide sequence.
  • blastn: nucleotide query against a nucleotide database.
  • tblastn: protein query against a nucleotide database translated in all six reading frames.
  • tblastx: nucleotide query, translated in all six frames, against a nucleotide database also translated in all six frames.

  Several programs also offer variants:

  • -fast (for example blastx-fast, blastp-fast, tblastn-fast): a faster preset that uses a larger word size, best suited to finding closely related sequences at the cost of sensitivity for distant matches.
  • -short (for example blastp-short, blastn-short): tuned for short query sequences, using a smaller word size and adjusted scoring.
  • megablast (a blastn mode): the fastest nucleotide search, for highly similar sequences such as those within a species.
  • dc-megablast (discontiguous megablast, a blastn mode): for more divergent nucleotide sequences, such as cross-species comparisons.

  Only searches against a protein database (blastp, blastx) produce hits usable for GO mapping and annotation, since Gene Ontology terms are linked to proteins. Default: blastx-fast. * Blast DB. The database to search in. The field is an editable list pre-populated with common NCBI databases (for example nr, swissprot, refseq_protein, pdb, and nt); any other valid NCBI database name can also be entered. Default: nr. For the full list of protein databases available at NCBI, see this reference. * Taxonomy Filter. Search for Blast results only in the selected taxonomy. * Blast Expectation Value (e-Value). The statistical significance threshold for reporting matches. Matches whose statistical significance is greater than the threshold are not reported. Lower thresholds are more stringent. * Number of Blast hits. The number of alignments to report (0-100). * Blast Description Annotator. The BDA finds the best possible description for a new sequence based on a given Blast result.

The Advanced page provides additional parameters:

• Word Size. The length of the initial word of the local alignment. Smaller values increase sensitivity; larger values increase speed. Default: 6 (for blastx-fast).
• Low Complexity Filter. Applies SEG filtering of low-complexity protein regions before the search.
• HSP Length Cutoff. The minimal length of the first HSP of a hit, used to exclude hits with only small local alignments.
• HSP-Hit Coverage. The minimum percentage of the hit that its best HSP must cover (0-100). The default 0 means no filter.
• Filter by Description. Removes hits whose description contains the given text (semicolon-separated terms).

On the Save Results page, the results can be saved in four formats, each to its own output folder: XML2 (enabled by default), XML, TXT, and HTML.

Results

Sequences with hits turn orange and sequences without hits turn dark red in the functional annotation project. The Blast statistics charts, Blast side-panel actions, and the individual Blast result view are described in the Blast Search Results section.

OmicsBox Engine

This tool can be run from the command line via the OmicsBox Engine.

Command: omicsbox ncbi-blast [options]
Execution: Local (runs on your machine)

Inputs

Parameters

Global options (--local-folder, --cloud-folder, --output-format, --config, --detach, --verbose, …) are shared by every Engine tool and are not repeated here — see the OmicsBox Engine reference.