NCBI Blast - Local

Introduction

Local Blast searches the project sequences against a local database on the same machine. OmicsBox can build a Blast database from a FASTA file with the Create Blast Database tool. Databases must be formatted for NCBI Blast+.

Local Blast 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.

Please cite NCBI for Local Blast and pre-formatted databases: https://www.ncbi.nlm.nih.gov/books/NBK569850/.

Run

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

• 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. * Strand. Whether to search both strands, only the forward strand, or only the reverse strand. Available only for blastx and blastx-fast. * Formatted Blast Database. The local database to search against. Choose any file of a database formatted for NCBI Blast+ (.psq, .nsq, .pal, or .nal); the path must not contain spaces. Use Create Blast Database to build a database from a FASTA file. * 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 (1-500). * Blast Description Annotator. Finds the best possible description for each sequence from its Blast result. * Word Size. The length of the initial word of the local alignment. Smaller values increase sensitivity; larger values increase speed. * Low Complexity Filter. Applies SEG filtering of low-complexity protein regions before the search. * Number of Threads. The number of CPU cores to use; more threads run faster. By default all available cores are used. * HSP Length Cutoff. The minimal length of the first HSP of a hit, used to exclude hits with only small local alignments. * Filter by Description. Removes hits whose description contains the given text (semicolon-separated terms). * Blast XML2 Folder. If checkec, the results are saved as XML2 files in the selected output folder.

See this tutorial on how to download NCBI pre-formatted databases.

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.