1. Overview

GOMAP-singularity is the containerized version of the Gene Ontology Meta Annotator for Plants (GOMAP) pipeline. GOMAP is a high-throughput pipeline to annotate GO terms to plant protein sequences. The pipeline uses three different approaches to annotate GO terms to plant protein sequences, and compile the annotations together to generate an aggregated dataset. GOMAP uses Python code to run the component tools to generate the GO annotations, and R code to clean and aggregate the GO annotations from the component tools.

The GOMAP-singularity container is designed with two uses in mind, namely reproducability and portability. The pipeline development is still ongoing and the major bugs are fixed. We have prioritized the quality of the dataset over other features. Some anotations tools are which produce good annotations are not available in a containerized format, so the pipeline cannot be converted into a self-contained container. As new members are added to the team, and more tools are evaluated we may update the pipeline to be self-contained in future.

1.1. Methods used in GOMAP

1. Sequence-similarity

   Sequence-similarity methods search for similar sequences in other species for the given input sequences, and inheric curated/reviewed GO terms from other species to maize. Two datasets are used for the sequence-similarity datasets namely Arabidopsis and UniProt .

2. Domain-presence

   Domains-presense method searches for known protein domains and signatures in the input sequences and assign GO terms from curated domains and signatures to the input sequences

3. Mixed-methods

   Mixed-methods or CAFA tools used in the pipeline were Argot2 and PANNZER. Both tools use information generated from sequence-similarity and domain presence to predict better Annotations from the dataset.

1.1.1. Sequence-similarity

1.1.1.1. Arabidopsis

Sequence-similarity search is performed against Arabidopsis protein sequences downloaded and curated/reviewed annotations downloaded from TAIR [1]. The exact steps used for annotations are given below.

1.1.1.2. UniProt

Sequence-similarity search is performed against plant protein sequences for the top 10 annotated plant species. The protein sequences and curated/reviewed annotations were downloaded from QuickGO [2][3][4]. The exact steps used for annotations are given below.

1.1.2. Domain-presence

Domain-presence step uses InterProScan to search for signatures present in the input sequences and annotate GO terms to protein sequences. InterProScan-5.25-64.0 was downloaded from https://github.com/ebi-pf-team/interproscan/wiki and used to annotate input sequences [5].

1.1.3. Mixed-methods

Three mix-methods have been used in GOMAP, namely Argot2.5, FANN-GO and PANNZER [6][7][8]. Argot2.5 and PANNZER require preprocessing if the input sequences before they can be used to annotate GO terms to input sequences. The overall steps for running the mixed-methods have been given in the diagram below.

The main step common to Argot2.5 and PANNZER tools is the mixmeth-blast. This runs the BLASTP search against UniprotDB and creates the XML output for chunked input [9][2]. The XML files from the mixmeth-blast are used for annotation with PANNZER tool. The XML files are converted to CSV for Argot2.5. The Argot2.5 also requires Pfam hits for the input sequences from HMMER. These two files are submitted to Argot2.5 webserver for annotation. The annotations are retrieved after job completion emails are sent by Argot2.5.

1.2. Datasets used in GOMAP

1.2.1. Public datasets used in GOMAP

Database	Type	Format	Version	Species	Citation
TAIR	Protein Sequences	fasta	TAIR 10	Arabidopsis thaliana	[1]
TAIR	GO Annotations	gaf 2.0	TAIR 10 (20170410)	Arabidopsis thaliana	[1]
Gramene 49	Gene Annotations	gff3	5b+	Zea mays	[10]
Gramene 49	GO Annotations	gaf 2.0	5b+	Zea mays	[10]
Phytozome 11	GO Annotations	tsv	5b+	Zea mays	[11]
Uniprot	Protein sequences	fasta	20170410	All species	[2]
Uniprot	Protein sequences	fasta	20170410	All plants	[2]
Uniprot	GO Annotations	gaf 2.0	20170410	All plants	[3][4]
Pfam	HMMs	hmm	27.0	All species	[12]
PANTHER	HMMs	hmm	10.0	All species	[13]

1.2.2. Software tools used in GOMAP

Software	Type	Version	Citation
NCBI-BLAST	Sequence similarity	2.6.0	[9]
HMMER	HMM scanning	3.1b1	[14]
InterProScan5	GO Annotation	5.15-55.0	[5]
PANNZER	GO Annotation	1.1	[8]
Argot2	GO Annotation	2.5 (Server)	[6]
FANN-GO	GO Annotation	1 version	[7]
AIGO	GO Evaluations	0.1.0	[15]

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