GO Mapping

Group

Analysis

Argument

-mapping

Short Description

Run GO Mapping.

Description

Mapping is the process of retrieving GO terms associated with the Hits obtained by the BLAST search. OmicsBox performs four different mappings steps:

  1. BLAST result accessions are used to retrieve gene names or symbols making use of two mapping files provided by the NCBI (gene_info, gene2accession). Identified gene names are then searched in the species-specific entries of the gene-product table of the GO database.

  2. GeneBank identifiers (gi), the primary blast Hit ids, are used to retrieve UniProt IDs making use of a mapping file from PIR (Non-redundant Reference Protein Database) including PSD, UniProt, Swiss-Prot, TrEMBL, RefSeq, GenPept and PDB.

  3. Accessions are searched directly in the dbxref table of the GO database.

  4. BLAST result accessions are searched directly in the gene-product table of the GO database.

It is necessary to follow the Installation instructions on “Setting up a local Blast2GO Mapping Database” before.

Requirements

  • Access to a local MongoDB server with a GO Mapping database collection installed.

  • Load a sequence project in the same command, e.g. Blast .XML file or .box containing sequence data with Blast results.

Properties File

LocalBlastAlgoParameters