AnnoTALE

Transcription activator-like effectors (TALEs) are virulence factors of plant-pathogenic Xanthomonas spp. that function as gene activators inside plant host cells.

AnnoTALE is a suite of applications for identifying and analysing TALEs in Xanthomonas genomes, for clustering TALEs into classes by their RVD sequences, for assigning novel TALEs to existing classes, for proposing TALE names using a unified nomenclature, and for predicting targets of individual TALEs and TALE classes.

AnnoTALE is available as a JavaFX-based stand-alone application with graphical user interface for interactive analysis sessions. In addition, we provide a command line application that may be integrated into other pipelines. Both use identical code for the actual analysis, ensuring consistent results between both versions.

AnnoTALE with GUI

AnnoTALE is based on the very recent implementation of JavaFX in Java 8.

We provide AnnoTALE as a runnable JAR file for those with a current version of Java 8 (at least update 45) on their machine.

For user's convenience, we also provide pre-packaged versions of AnnoTALE, which also include Java in the required version, for Mac OS X and Windows. Each of these versions is available two version with different memory requirements (2GB and 6GB). As long as the main memory (RAM) of your machine is sufficient, we recommend to use the 6GB version of AnnoTALE.

Download

AnnoTALE is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.

• Runnable Jar (requires Java 8, update 45 or greater)
• Mac-DMG of AnnoTALE including Java: 2GB version, 6GB version
• Windows installer of AnnoTALE including Java: 1GB version, 2GB version, 6GB version

User Guide

We provide an AnnoTALE User Guide in PDF format, including a detailed description of all AnnoTALE tools and installation instructions.

AnnoTALE command line application

The AnnoTALE command line application is available as a runnable Jar. For running the program and a quick help, type

java -jar AnnoTALEcli-1.0.jar

For larger analyes, it might be necessary to increase the memory allocated by the JavaVM using the -Xms and -Xmx parameters, for instance

java -Xms512M -Xmx6G -jar AnnoTALEcli-1.0.jar

There is no separate User Guide for the AnnoTALE command line application, but the User Guide for the GUI version describes all AnnoTALE tools, their parameters and outputs, and those of the CLI version are identical.

You obtain a list of all AnnoTALE tools by calling

java -jar AnnoTALEcli-1.0.jar

Output:

Available tools:

	predict - TALE Prediction
	analyze - TALE Analysis
	build - TALE Class Builder
	loadAndView - Load and View TALE Classes
	assign - TALE Class Assignment
	rename - Rename TALEs in File
	targets - Predict and Intersect Targets

Syntax: java -jar AnnoTALEcli-1.0.jar <toolname> [<parameter=value> ...]

Further info about the tools is given with
	java -jar AnnoTALEcli-1.0.jar <toolname> info

Tool parameters are listed with
	java -jar AnnoTALEcli-1.0.jar <toolname>

You get a list of input parameters by calling AnnoTALEcli-1.0.jar with the corresponding tool name, e.g.,

java -jar AnnoTALEcli-1.0.jar predict

Output:

At least one parameter has not been set (correctly):

Parameters of tool "TALE Prediction" (predict):
g - Genome (The input Xanthomonas genome in FastA or Genbank format)	= null
s - Strain (The name of the strain, will be used for annotated TALEs, OPTIONAL)	= null
outdir - The output directory, defaults to the current working directory (.)	= .

You get a description of each tool by calling AnnoTALEcli-1.0.jar with the corresponding tool name and keyword "info", e.g.,

java -jar AnnoTALEcli-1.0.jar predict info

Output:

*TALE Prediction* predicts transcription activator-like effector (TALE) genes in an input sequence, typically a 'Xanthomonas' genome.

'TALE Prediction' is based in HMMer nucleotide HMM models that describe N-terminus, repeat region, and C-terminus of TALEs.

The input 'Genome' may be provided in FastA or Genbank format. 
Optionally, you may provide a strain name that will be used in the temporary TALE names and names of output files.

Regardless of the input format, 'TALE Prediction' generates output in Genbank format containing the annotations of TALE genes. If the original input has already been a Genbank file, TALE annotations are added to the existing ones.
In addition, 'TALE Prediction' generates annotations in GFF format, and also outputs the DNA and AS sequences of the predicted TALEs in FastA format.

'TALE Prediction' tries hard to make the CDS annotation a proper gene model, starting from a start codon and ending with a Stop. If either start or stop codon are located within the originally predicted region that is homologous to TALE genes, this original hit region is still reported as mRNA.
Putative pseudo genes, e.g., with premature stop codons, are marked accordingly.

The TALE DNA sequences output of 'TALE Prediction' may serve as input of the 'TALE Analysis', 'TALE Class Builder', and 'TALE Class Assignment' tools.

If you experience problems using 'TALE Prediction', please contact us.

Standard pipeline

Assuming that your current working directory contains the AnnoTALEcli Jar file, a genome of interest (of a hypothetical 'Xoo' strain PXO999 with accesion CP1234567) in a FastA file "genome.fa", all rice promoters in a FastA file "Rice-promoters.fa", and a directory "out" designated to hold all output files, a typical AnnoTALE pipeline could look like

java -jar AnnoTALEcli-1.0.jar predict g=genome.fa outdir=out

java -jar AnnoTALEcli-1.0.jar analyze t=out/TALE_DNA_sequences.fasta outdir=out

java -jar AnnoTALEcli-1.0.jar loadAndView outdir=out

java -jar AnnoTALEcli-1.0.jar assign c=out/Class_builder_download.xml t=out/TALE_DNA_parts.fasta s="Xoo PXO999" a="CP1234567" outdir=out

java -jar AnnoTALEcli-1.0.jar rename r=out/TALE_names_\(Xoo_PXO999\).tsv i=out/Genbank__TALE_predictions.gb outdir=out

java -jar AnnoTALEcli-1.0.jar targets i=Rice-promoters.fa p="TALEs in class builder" c=out/Augmented_class_builder_\(Xoo_PXO999\).xml outdir=out

Afterwards, you find all output files of all those tools in the directory "out". The output files and directories are named in analogy to the names in the AnnoTALE GUI version (see User Guide for the GUI version)