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OrthoInspector v2.21: New option in the Uniprot utility (11/08/2015)

* OrthoInspector_uniprot_tools.jar

An option was added to ignore the correction of the gene redundancy (only the longest transcript per gene was kept). Filtered sequences are now mentionned in a log file.  See tutorial for details.


OrthoInspector v2.20: New tool to build OrthoInspector inputs from Uniprot reference proteomes (06/08/2015)

+ Addition of a new utility: OrthoInspector_uniprot_tools.jar

This tool facilitates the initial selection of a panel of organisms to create the orthology database. Currently, it does some checkups for the Uniprot fasta proteomes and generates the corresponding organism.xml and fasta files which are used as inputs in the first step of OrthoInspector installation. A new website tutorial details its use.

* Graphical interface:

Some corrections in the phylogenetic profile tool, related to errors when duplicated names occur in some NCBI Taxonomy phylums (mostly when sub-genus have the same name as the genus).

* All:

Minor bug fixes.


What is OrthoInspector ?

OrthoInspector is a package dedicated to orthology inference and analysis. The package can be installed for local use on a desktop computer or configured for a server implementation. Its purpose is to facilitate the installation of a database of newly inferred orthology relations and facilitate the exploitation of the resulting orthology database by both expert and non-expert users.

What are the requirements ?

OrthoInspector is compatible with all systems supporting Java 1.6.x JVM and superior. Its components are based on a  SQL database / Java client architecture. Consequently, you need to setup an access to an SQL engine (locally or remotely). Any database engine can be used as soon as a Java JDBC driver is available for it. (see complete Requirements for details). Exploiting the inferred orthologs will also require a local installation of the latest NCBI blast+ package.

Why do I need a SQL database ?

While the package can be installed on a single machine, we choose to code OrthoInspector in Java and through a SQL database / Java client architecture to facilitates its exploitation in a network environment. Orthlogy relations are first predicted from a set of proteomes and a blast all-against-all and are transferred to an SQL database. Then, these relations can be exploited by several clients, allowing several users to query the database via a graphical interface or allowing several pipelines to exploit these data simultaneously.

Be aware that OrthoInspector can be installed either on a network or on a single desktop computer !
You just need to setup an accessible SQL engine, locally (desktop computer) or remotely (office network).
The network configuration described below is a recommendation but can be adapted to your needs.



How is organized the package and what can I do with it ?

The package is separated in three Java executables (and a few configuration files) :

  • Installation command-line: A command-line to predict orthology relations and transfer them in a SQL database.
  • Query command-line: A command-line to query these predictions or export them from the database.
  • Graphical interface: a desktop interface which regroup most high-level functionnalities (complex queries and visualisation tools) but can also be used directly to infer small orthology datasets (<100 species).

Both the Installation command-line and the Graphical interface can be used to infer orthology relations. The query command-line and most other functions from the graphical interface are designed to exploit these predictions.

Installation command-line:

This component is recommended to infer large orthology databases from large datasets (> 100 species). A similar procedure is available in the graphical interface but the Installation command line provides several useful options to handle larger datasets. For instance, it can read compressed blast inputs, create compressed outputs, share predictions to several CPUs and facilitate crash recovery (useful when your calculations require a weeks of CPU...).

Query command-line:

This component is designed for basic data retrieval from the orthology database. You can query the databases with textual searches, fasta queries or export the entire set of orthologs related to a particular organism. It can easily be integrated into other bioinformatic pipelines.

Graphical interface:

Contains most functionalities and is a good option for non-specialists which want to avoid command-line manipulations (but you still need to install and configure the SQL database). You can install a small database (<100 organisms) with an automated procedure. This procedure is fully automated if you use MySQL or Postgresql engines. The graphical interface contains advanced querying tools, such as sequence extractions  based on phylogenetic profiles. All the graphical tools dedicated to orthology analysis and visualization (Euler diagrams, automated phylogenetic profile construction...) are also in the Graphical interface.

To know more about these tools, consult the dedicated tutorials which are available on this website.



What about the online databases ?

We have pre-computed 3 orthology databases, exploring most known clades:

  • Eukaryotes: 256 eukaryotes, from unicellular species to animals, plants and fungi.
  • Prokaryotes: 1688 species from most known groups.
  • Quest for orthologs: a mix of 150 prokaryotes and eukaryotes, based on the Quest for Ortholog consortium benchmark.

All databases can be accessed and browsed from the "database" menu of this website. The online databases doesn't provide the extended functions of the OrthoInspector package but allow you to retrieve specific orthology relations via textual and Blast searches. The whole content the database can also be downloaded in CSV and ORTHOXML formats. We do not provided raw SAL dumps of these databases (several hundreds of gigabytes, each of them...). However, if you desire a copy of these databases for a specific project (you can then immediately use them through Orthoinspector clients), please contact Odile Lecompte ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ).

Distribution and modifications.

OrthoInspector is licensed under the GNU GPL version 3. You can download it, modify it and share it at your convenience but don't forget to cite the authors ! ;-)



Last updates


OrthoInspector v2.15 Bugfixes (23/06/2015)

* All tools:

Embedded property files have been removed, forcing the user to correctly configure local property files. New error messages help to verify that OrthoInspector is attempting to load the correct property files ('/path/to/' errors, due to unconfigured oi_client.properties files, are now gone). Several other minor bug fixes.


OrthoInspector v2.14 Bugfixes (1/09/2014)

* Graphical interface:

Bug correction in the VennEuler diagram interface.

* MySQL database dump:

Spelling correction in the MySQL database dumps. This error only occurred in a MySQL-based installation. The Best-hit density graph was crashing, the 'Hit' table had a column called 'pk_sequence_hit' instead of the expected 'pk_sequence' column).


OrthoInspector v 2.13 - Bugfixes (18/07/2014)


* Command-line: Correction of some bugs introduced with multi-threading options. The last step (orthology calculation) was crashing in some circumstances.


*  Several minor bugs corrections


OrthoInspector v 2.12 - Bugfixes (7/05/2014)

+ Tutorial for multi-threading installations
* Correction of some bugs introduced with -orgaid_start -orgaid_end options

*  Several minor bugs corrections


OrthoInspector v 2.11 - Bugfixes and (virtual) multi-threading (7/04/2014)

+ 2 new parameters (-orgaid_start -orgaid_end) are introduced to simulate multi-threading in inparalogy and orthology calculation steps. (see archive manual)

* Correction of a textual search bug that couldn't select the good sequence for queries such as 'mtr1' 'mtr11'
*  Several minor bugs corrections


OrthoInspector v 2.10 - Introduction of GZIP support and bugfixes (15/07/2013)

+ database dumps can now be automatically compressed GZIP format (option -gzip_dumps)
+ blast inputs can be GZIP compressed files, orthoinspector automatically detects if the blast is compressed.

* correction of the bugs introduced in 2.00 major update.


OrthoInspector v 2.00 - Major update (5/02/2013)

A new major version of OrthoInspector is now released. It is focused on interface improvements for a more user-friendly navigation. No changes were done on the orthology prediction algorithm. Consequently, the command-line binaries are quite similar to previous versions.
The tutorials of the website will be regularly updated with screenshots of the new interface.

Major software improvements:

+ Interactive tree to select organisms and whole phylums directly.
+ Customized version of interactive species tree to build more easily phylogenetic profiles during protein family extraction. (see tutorial)
+ New layout for the main interface
+ Better handling for data export, with dedicated menus.
+ New visualisation tool to generate and then modify phylogenetic profiles. (see tutorial)
+ Better error handling, with more understandable error messages in command-line tools.
+ Many other small bugfixes since version 1.40

Online database:

+ Release of the second version of the online database (it contains now 259 eukaryotic species).
+ Interactive Tree to facilitate species selection.
+ Display of protein isoforms, based on Uniprot gene annotations.

We would be grateful for your replies if you find new bugs in this major release. Smile


New website section - "Reference proteomes" (09/07/2012)

Following the "Quest for Orthologs" consortium recommandations, several curated reference proteomes are now freely available in EBI ftp. Orthology calculations based on these datasets can be downloaded from "Reference proteomes" menu.


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