GeMoMa

by Jens Keilwagen, Michael Wenk, Jessica L. Erickson, Martin H. Schattat, Jan Grau, and Frank Hartung

Gene Model Mapper (GeMoMa) is a homology-based gene prediction program that uses the annotation of protein-coding genes in a reference genome to infer annotation of protein-coding genes in a target genome.

Abstract

Annotation of protein-coding genes is very important in many fields of research and application. Thereby, homology-based gene prediction programs allow for transferring knowledge from an annotated organism to an organism of interest.

Here, we present a homology-based gene prediction program called GeMoMa. GeMoMa utilizes the intron position conservation of related genes in different organisms. We assess the performance of GeMoMa comparing it with state-of-the-art competitors on plant and animal genomes using an extended best reciprocal hit approach. We find that it often makes more precise predictions than its competitors yielding an improvement of up to 622% more correct transcripts. Subsequently, we use RNA-seq data to compare the predictions of homology-based gene prediction programs, and find again that GeMoMa performs well.

Hence, we conclude that exploiting intron position conservation improves homology-based gene prediction, and we make GeMoMa freely available as command-line tool and Galaxy integration.

Paper

If you use GeMoMa, please cite

J. Keilwagen, M. Wenk, J. L. Erickson, M. H. Schattat, J. Grau, and F. Hartung. Using intron position conservation for homology-based gene prediction. Nucleic Acids Research, 2016. doi: 10.1093/nar/gkw092

Web-server

GeMoMa is available in a public web-server at galaxy.informatik.uni-halle.de. The provided web-server only allows a limited number of reference genes and uses a time out of 2 minutes per transcript prediction. For unlimited use, please use the command line program or integrate GeMoMa in your only Galaxy instance.

Download

GeMoMa is implemented in Java using Jstacs. You can download a zip file containing a readme, the GeMoMa jar file and some tiny scripts for running GeMoMa. The jar file allows for

• running the command line interface (CLI) version
• creating the XML file needed for the Galaxy integration.

Running the command line application

For running the command line application, Java v1.6 or later is required.

For preparing the data, we provide the tool Extractor. You can run Extractor from the command line with
java -jar GeMoMa-1.1.2.jar CLI Extractor [<parameter>=<value> ...]
The parameters comprise:

name	comment	type
a	annotation (Reference annotation file (GFF), which contains gene models annotated in the reference genome)	FILE
g	genome (Reference genome file (FASTA))	FILE
gc	genetic code (optional user-specified genetic code, OPTIONAL)	FILE
p	proteins (whether the complete proteins sequences should returned as output, default = false)	BOOLEAN
t	transcripts (whether the complete transcripts sequences should returned as output, default = false)	BOOLEAN
s	selected (The path to list file, which allows to make only a predictions for the contained transcript ids. The first column should contain transcript IDs as given in the annotation. Remaining columns will be ignored., OPTIONAL)	FILE
v	verbose (A flag which allows to output wealth of additional information, default = false)	BOOLEAN
outdir	The output directory, defaults to the current working directory (.)	STRING

For predicting gene models, we provide the tool GeMoMa. You can run GeMoMa from the command line with
java -jar GeMoMa-1.1.2.jar CLI GeMoMa [<parameter>=<value> ...]
The parameters comprise:

name	comment	type
t	tblastn results (The sorted tblastn results)	FILE
tg	target genome (The target genome file (FASTA), i.e., the target sequences in the blast run)	FILE
c	cds parts (The query cds parts file (FASTA), i.e., the cds parts that have been blasted)	FILE
a	assignment (The assignment file, which combines parts of the CDS to transcripts, OPTIONAL)	FILE
q	query proteins (optional query protein file (FASTA) for computing the optimal alignment score against complete protein prediction, OPTIONAL)	FILE
g	genetic code (optional user-specified genetic code, OPTIONAL)	FILE
s	substitution matrix (optional user-specified substitution matrix, OPTIONAL)	FILE
go	gap opening (The gap opening cost in the alignment, default = 11)	INT
ge	gap extension (The gap extension cost in the alignment, default = 1)	INT
m	maximum intron length (The maximum length of an intron, default = 15000)	INT
i	intron-loss-gain-penalty (The penalty used for intron loss and gain, default = 25)	INT
e	e-value (The e-value for filtering blast results, default = 100.0)	DOUBLE
ct	contig threshold (The threshold for evaluating contigs, valid range = [0.0, 1.0], default = 0.9)	DOUBLE
r	region threshold (The threshold for evaluating regions, valid range = [0.0, 1.0], default = 0.9)	DOUBLE
h	hit threshold (The threshold for adding additional hits, valid range = [0.0, 1.0], default = 0.9)	DOUBLE
p	predictions (The (maximal) number of predictions per transcript, default = 1)	INT
selected	selected (The path to list file, which allows to make only a predictions for the contained transcript ids, OPTIONAL)	FILE
as	avoid stop (A flag which allows to avoid stop codons in a transcript (except the last AS), default = true)	BOOLEAN
approx	approx (whether an approximation is used to compute the score for intron gain, default = true)	BOOLEAN
align	align (A flag which allows to output a tab-delimited file, which contains the results in a blast-like format (deprecated), default = false)	BOOLEAN
genomic	genomic (A flag which allows to output a fasta file containing the genomic regions of the predictions, default = false)	BOOLEAN
prefix	prefix (A prefix to be used for naming the predictions, default = )	STRING
tag	tag (A user-specified tag for transcript predictions in the third column of the returned gff. It might be beneficial to set this to a specific value for some genome browsers., default = prediction)	STRING
v	verbose (A flag which allows to output wealth of additional information per transcript, default = false)	BOOLEAN
outdir	The output directory, defaults to the current working directory (.)	STRING

GeMoMa returns the predicted annotation as gff file and the predicted proteins as fasta file.

Version history

GeMoMa 1.1.2 (06.06.2016)

• minor modifications to the Extractor tool

[1] (05.02.2016)

• GeMoMa bugfix (upstream, downstream sequence for splice site detection)
• Extractor: new parameter s for selecting transcripts
• improved Galaxy integration

GeMoMa 1.1.1 (01.02.2016)

• initial release for paper