BIND and MIND: Gene prediction and optimization

Introduction

MIND: ab initio gene predictions by MAKER combined with gene predictions INferred Directly from alignment of RNA-Seq evidence to the genome.

BIND: ab initio gene predictions by BRAKER combined with gene predictions INferred Directly from alignment of RNA-Seq evidence to the genome.

Overview

You will need an diverse, orphan-enriched RNA-Seq dataset from NCBI-SRA (as available) and the genome sequence of your species of interest. Run an ab initio prediction either by BRAKER or by MAKER (we provide Singularity containers to facilitate installation of these pipelines). Run the evidenced-based Direct Inference pipeine. Combine the ab initio predictions with the Direct Inference predictions using Mikado. Evaluate your predictions

Tutorial

See the detailed scripts here .

Contents

• Find an Orphan-Enriched RNA-Seq dataset from NCBI-SRA
• Ab initio predictions
• Direct Inference evidence-based predictions
• Combine ab initio and Direct Inference evidence-based predictions
• Downstream analysis to evaluate and annnotate gene predictions

Tools used for prediction

Tool	Purpose
SRA Tools (v. 2.9.6 )	SRA access
Hisat2 (v. 2.2.0)	Alignment
STAR (v. 2.7.7a)	Alignment
Kallisto (v. 0.46.2)	Quantification
Samtools (v. 1.10)	Tools
CLASS2 (v. 2.1.7)	Transcript Assembly
Stringtie (v. 1.3.3)	Transcript Assembly
Cufflinks (v. 2.2.1)	Transcript Assembly
Trinity (v. 2.6.6)	Transcript Assembly
Porticullis (v. 1.2.2)	Tools
Transdecoder (v. 3.0.1)	CDS prediction
Mikado (v. 2.0)	Direct Inference prediction
Phylostratr (v. 0.2.0)	Phylostratigraphy
BLAST (v. 3.11.0)	Tools
Braker (v. 2.1.2)	Ab initio prediction
Maker (v. 2.31.10)	Ab initio prediction
GMAP-GSNAP (v. 2019-05-12)	Alignment
GeneMark (v. 4.83)	Ab initio Prediction