CloudBlast Against Custom Database

Introduction

CloudBlast Against Custom Database runs Blast against a database made from a custom protein FASTA file, using the OmicsBox cloud resources. The database is generated automatically in the cloud from the FASTA file and the parameters provided. Running CloudBlast Against Custom Database consumes Cloud Units (see the CloudBlast page for more information on Cloud Units).

CloudBlast Against Custom Database 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 Custom Database on the first page of the Blast wizard. The wizard first defines the custom database, then the Blast parameters.

The custom database is defined with:

• Database FASTA File(s). The protein FASTA file(s) used to build the database in the cloud.
• Database Name (optional). A name for the database, shown as the target database in the result header. Only letters, numbers, underscores, and hyphens are allowed.
• Enable --parse_seqids. Retrieves extra information from the sequence IDs and descriptions. It may fail with FASTA headers that do not follow the NCBI style. Enabled by default.
• Database Sequences Taxonomy ID. A single taxonomy ID assigned to all database sequences (0 for none).
• Database Taxonomy IDs Map File. As an alternative to a single ID, if checked a file mapping each sequence ID to its taxonomy ID (no header) has to be provided.

The Blast parameters are:

• Blast BlastMode. The Blast algorithm, chosen according to the type of the query sequences. Because the custom database is a protein database, the available 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.

  Both programs also offer variants:

  • -fast (blastx-fast, blastp-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 (blastp-short): tuned for short query sequences, using a smaller word size and adjusted scoring.

  Default: blastx-fast. * Blast Expectation Value (e-Value). The statistical significance threshold for reporting matches. Lower values are more stringent. * Number of Blast Hits. The number of alignments to retrieve (1-100). * Blast Description Annotator. Finds the best possible description for each sequence from its Blast result. Enabled by default. * 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 minimum alignment length of an HSP, used to exclude hits with only short local alignments (1-5000). HSPs shorter than this value are discarded, and a hit is excluded when none of its HSPs reaches it. The length is the number of aligned positions in amino acids, gaps included. Hits whose database sequence is shorter than this value are also excluded. Default: 33. * HSP-Hit Coverage. The minimum percentage of the hit sequence that one of its HSPs must cover, measured over the region of the hit that the HSP aligns to (0-100). Only HSPs that pass the HSP Length Cutoff count. For example, 80 keeps a hit only if at least one of its HSPs spans 80% or more of the hit length. Low values are recommended: most low-coverage hits come from short or partial query sequences matched against longer database sequences. Hits without subject coordinates are not removed by this filter. Default: 0 (no filter). * Filter by Description. Removes hits whose description contains the given text. Separate several terms with semicolons. Terms are case-sensitive, and a single term is also matched against the hit ID. * Save results locally. If checked, the results are saved as XML2 files in the selected output folder.

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 cdblast [options]

Input constraint: provide exactly one of: --i-local-project, --i-input-fasta.

Inputs

Parameters

Parameter relationships

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.