Resource Type
ZEAMAP Genomics: Gene Functional Annotation

For each genome annotation, the protein sequences of the predicted genes were compared against the InterPro database using InterProScan 5 to identify functional protein domains. The proteins were further compared against the GenBank non-redundant protein (nr) database using Basic Local Alignment Search Tool (BLAST) with the options “-p blastp –e 1e-05 –b 5 –v 5 –a 4 –m 7 –F F”. The BLAST results against the nr database and the Interpro results were further analyzed by Blast2GO to assign gene ontology (GO) terms. annotations were performed by running BLAST against the KEGG database (version 84.0) with options “-p blastp -e 1e-05 -a 4 -m 8 -F F”. The proteins were also searched against PFAM version 32.0 using HMMer 3.1b2 with default parameters. To identity gene orthologs and clusters of orthologous group (COG) annotations, the proteins were mapped to eggNOG orthology database (version 4.5.1) using emapper-1.0.3. To add gene-product annotations, the proteins were searched against UniProt database (version 2019_04) using Diamond (v0.8.22.84) with the options “--evalue 1e-05 --max-target-seqs 1”, the UniProt and EggNog search results were combined to get the gene and product names using Gene2Product v1.32. Possible proteolytic enzymes were annotated by searching the proteins against the MEROPS database (version 12.0) using Diamond with the options “--evalue 1e-05 --max-target-seqs 1”. The proteins were also searched against the BUSCO (version 2.0) dikarya models using HMMer with default options.

Program, Pipeline, Workflow or Method Name
A set of tools described in Description
Program Version
Date Performed
Monday, March 30, 2020 - 03:44
Data Source