GOanna
Runs BLASTp of a single peptide FASTA file vs phylogenetic subsets of Uniprot accessions provided by AgBase. Transfers gene ontology (GO) annotations to from BLASTp matches to the query gene productsKOBAS
KEGG Orthology Based Annotation System (KOBAS) is a standalone Python application in Bioinformatics. KOBAS can assign appropriate KO terms for queried sequences based on similarity search, and it can further discover
enriched KO terms among the annotation results by frequency of pathways or statistical significance of pathways.
Quick Start
- GOanna accepts a single peptide FASTA file.KOBAS accepts several file formats: FASTA, tabular BLAST output, IDs list (see documentation for details)
- Resources: https://agbase.arizona.edu/cgi-bin/tools/GOanna.cgi, https://github.com/AgBase/GOannakobas, https://agbase-docs.readthedocs.io/en/latest/
Test Data
| Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> GOannaKOBAS -> annotate |
Input File(s)
Use CFLO_1.fa from the directory above as test input.
Parameters Used in App
Use the Default these parameters with the Test data. Fill in the output section like so:
Output file basename: clfo1_vs_insecta
Database of query id: i5k
Assigned by field for your GAF output file: <your name>
Taxon ID of the peptide you are BLASTing: 29053test data:
select protein FASTA as the input file type
use 'dme' as the species code (Species codes can be looked up here: https://www.kegg.jp/kegg/catalog/org_list.html)
Output File(s)
clfo1_v_insecta.asn–BLAST output for conversion to other formats
clfo1_v_insecta.html–pairwise alignments from BLAST search
clfo1_v_insecta.tsv--tab-delimited BLAST output
clfo1_v_insecta_goanna_gaf.tsv–gene association file with transferred GO annotations
seq_pep folder --contains the BLAST database files that were used
- dme.pep.fasta (and corresponding .phr, pin, pog, psd, psi, psq files)
sqlite3–contains the database files used to annotate your data
- dme.db
- organism.db
dme.tsv–tabular BLAST output
kobas_annotate_out.txt–KOBAS annotate output (this can be used as input for KOBAS identify)