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.

If you use AnnoTALE, please cite:

Jan Grau, Maik Reschke, Annett Erkes, Jana Streubel, Richard D. Morgan, Geoffrey G. Wilson, Ralf Koebnik and Jens Boch. AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences. Scientific Reports 6:21077, DOI: 10.1038/srep21077, 2016.

For evolution-related studies using the comparative features of AnnoTALE, please also cite:

Annett Erkes, Maik Reschke, Jens Boch, and Jan Grau. Evolution of transcription activator-like effectors in Xanthomonas oryzae. Genome Biology and Evolution, 9(6):1599–1615, 2017.

If you use PrediTALE for predicting TALE targets, please also cite:

Annett Erkes, Stefanie Mücke, Maik Reschke, Jens Boch, and Jan Grau. PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting. PLOS Computational Biology, 15(7):1–31, 2019.

Important: If you would like to use the unified nomenclature of AnnoTALE in one of your publications including new TALEs or sequenced genomes, please contact us (grau@informatik.uni-halle.de) to organize the inclusion of your TALEs into the official class definition of AnnoTALE and to create stable TALE names that are unique to your TALEs.

AnnoTALE with GUI

AnnoTALE is based on the 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 installed Java >= 8, update 45), may be run under Linux, macOS and Windows
• macOS app: 2GB version, 6GB version, ZIP archive containing a macOS app including AnnoTALE and all required Java modules. For running this app, it might be required to explicitly give it running permissions in "System Preferences" -> "Security & Privacy" -> "General", which should list AnnoTALE after the first (possibly unsuccessful) starting attempt. Approve opening AnnoTALE by clicking on the button "Open Anyway" next to it.
• Windows installer of AnnoTALE including Java: 2GB version, 64bit Java, 6GB version, 64bit Java
• Windows version without installer: 6GB version, 64bit Java, ZIP archive containing AnnoTALE, all required Java modules, and a Windows batch file. For starting AnnoTALE, double-click AnnoTALE.bat.

Source code

The AnnoTALE source code is available from github.

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-1.5.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-1.5.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-1.5.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
	presence - TALE Class Presence
	repdiff - TALE Repeat Differences
	preditale - PrediTALE
	dertale - DerTALE

Syntax: java -jar AnnoTALEcli-1.5.jar <toolname> [<parameter=value> ...]

Further info about the tools is given with
	java -jar AnnoTALEcli-1.5.jar <toolname> info

Tool parameters are listed with
	java -jar AnnoTALEcli-1.5.jar <toolname>

You get a list of input parameters by calling AnnoTALEcli-1.5.jar with the corresponding tool name, e.g.,

java -jar AnnoTALEcli-1.5.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-1.5.jar with the corresponding tool name and keyword "info", e.g.,

java -jar AnnoTALEcli-1.5.jar predict info

Output:

A detailed description of all tools is available in the AnnoTALE User Guide (http://www.jstacs.de/downloads/AnnoTALE-UserGuide-1.0.pdf).

*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-1.5.jar predict g=genome.fa outdir=out

java -jar AnnoTALEcli-1.5.jar analyze t=out/TALE_DNA_sequences.fasta outdir=out

java -jar AnnoTALEcli-1.5.jar loadAndView outdir=out

java -jar AnnoTALEcli-1.5.jar assign c=out/Class_builder_download.xml t=out/TALE_DNA_parts.fasta s="Xoo PXO999" a="CP1234567" outdir=out

java -jar AnnoTALEcli-1.5.jar rename r=out/TALE_names_\(Xoo_PXO999\).tsv i=out/Genbank__TALE_predictions.gb outdir=out

java -jar AnnoTALEcli-1.5.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)

Version history

AnnoTALE

Version 1.5

• new "sensitive" mode of TALE Prediction tool, which may annotate TALEs in a wider range of Xanthomonas strains at the expense of an increased runtime; turned off by default
• significantly improved speed of TALE Class Assignment tool
• citation information for individual AnnoTALE tools available under a dedicated button in the GUI version and from the "info" command issued for individual tools in the command line version
• bugfix for TALE Prediction in rather fragmented genome assemblies, where TALE predictions may extend to the ends of contigs/sequences
• Runnable Jar (requires installed Java >= 8, update 45), may be run under Linux, macOS and Windows
• macOS app: 2GB version, 6GB version, ZIP archive containing a macOS app including AnnoTALE and all required Java modules. For running this app, it might be required to explicitly give it running permissions in "System Preferences" -> "Security & Privacy" -> "General", which should list AnnoTALE after the first (possibly unsuccessful) starting attempt.
• Windows installer of AnnoTALE including Java: 2GB version, 64bit Java, 6GB version, 64bit Java
• Windows version without installer: 6GB version, 64bit Java, ZIP archive containing AnnoTALE, all required Java modules, and a Windows batch file. For starting AnnoTALE, double-click AnnoTALE.bat.

Version 1.4.1

• first version to use the updated Class Builder including a large number of recently sequence strains
• minor changes to the output of the 'Load and View TALE Classes' tool, now including the accessions in the TALE sequence output
• changes to the Class Builder format to account for the increased size of class hierarchy, which previously resulted in unnecessarily large files
• 32bit/1GB Windows version no longer included
• 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: 2GB version, 64bit Java, 6GB version, 64bit Java
• AnnoTALE 1.4.1 command line application

Version 1.4:

• first version containing PrediTALE and DerTALE tools for target site prediction
• 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: 2GB version, 64bit Java, 6GB version, 64bit Java; in addition, we provide a 1GB version with 32bit Java for earlier and 32bit versions of Windows. Please use this version only if absolutely necessary, as some tools may not work due to memory restrictions.
• AnnoTALE 1.4 command line application

Version 1.3:

• AnnoTALE 1.3 Runnable Jar (requires Java 8, update 45 or greater)
• Mac-DMG of AnnoTALE 1.3 including Java: AnnoTALE 1.3 2GB version, AnnoTALE 1.3 6GB version
• Windows installer of AnnoTALE 1.3 including Java: AnnoTALE 1.3 2GB version, 64bit Java, AnnoTALE 1.3 6GB version, 64bit Java; AnnoTALE 1.3 1GB version with 32bit Java
• AnnoTALE 1.3 command line application

Changes:

• modified format of Class Builder files allowing for faster download using the "Load and View TALE Classes" tool; old Class Builder files can still be loaded
• "TALE Class Presence" now also outputs a phylogenetic tree of strains based on TALEome similarities

Version 1.2:

• AnnoTALE 1.2 Runnable Jar (requires Java 8, update 45 or greater)
• Mac-DMG of AnnoTALE 1.2 including Java: AnnoTALE 1.2 2GB version, AnnoTALE 1.2 6GB version
• Windows installer of AnnoTALE 1.2 including Java: AnnoTALE 1.2 2GB version, 64bit Java, AnnoTALE 1.2 6GB version, 64bit Java; AnnoTALE 1.2 1GB version with 32bit Java
• AnnoTALE 1.2 command line application

Changes:

• Results and loaded files may now be renamed in the GUI by clicking on the corresponding name in the "Data" panel
• Minor bugfixes and improvements of the GUI (Protocol may be erased, columns in "Data" panel renamed for clarity, consistency of paths in the open/save dialogs under Linux)
• Two new tools: "TALE Class Presence" and "TALE Repeat differences"

Version 1.1:

• AnnoTALE 1.1 Runnable Jar (requires Java 8, update 45 or greater)
• Mac-DMG of AnnoTALE 1.1 including Java: AnnoTALE 1.1 2GB version, AnnoTALE 1.1 6GB version
• Windows installer of AnnoTALE 1.1 including Java: AnnoTALE 1.1 2GB version, 64bit Java, AnnoTALE 1.1 6GB version, 64bit Java; AnnoTALE 1.1 1GB version with 32bit Java
• AnnoTALE 1.1 command line application

Changes:

• Additional output for the "Load and View TALE Classes" tool
• "TALE Class Builder" and "TALE Class Assignment" now also accept RVD sequences (separated by dashes) as input. However, this is not recommended and some features (e.g., highlighting of aberrant repeats) will not be available. Only complete TALE DNA sequences will be accepted for inclusion into the official Class Builder.
• The internal help pages now link to the PDF User Guide

Version 1.0:

Initial AnnoTALE release

• AnnoTALE 1.0 Runnable Jar (requires Java 8, update 45 or greater)
• Mac-DMG of AnnoTALE including Java: AnnoTALE 1.0 2GB version, AnnoTALE 1.0 6GB version
• Windows installer of AnnoTALE including Java: AnnoTALE 1.0 2GB version, 64bit Java, AnnoTALE 1.0 6GB version, 64bit Java; AnnoTALE 1.0 1GB version with 32bit Java
• AnnoTALE 1.0 command line application

Class Builders

• Version 29/07/2022: used for "Download current definition" in "Load and View TALE Classes" within AnnoTALE version 1.4.1 and later
• Version 17/08/2021: compatible with AnnoTALE version 1.4.1 and later
• Version 09/05/2021: compatible with AnnoTALE version 1.4.1 and later
• Version 10/10/2020: compatible with AnnoTALE version 1.4.1 and later
• Version 20/06/2019: compatible with AnnoTALE version 1.4.1 and later
• Version 29/09/2018: used for "Download current definition" in "Load and View TALE Classes" within AnnoTALE version 1.3 and later
• Version 09/03/2017: used for "Download current definition" in "Load and View TALE Classes" within AnnoTALE version 1.2 and earlier
• Version 03/11/2016
• Version 01/29/2016
• Version 10/19/2015: used in the AnnoTALE publication (Grau et al., Sci Rep, 2016)