A change in NCBI BLAST+ package v2.2.25 outputs broke the installation process in certain conditions. The header of the tab-formatted blasts outputs were not correctly parsed. The orthoinspector blast parser are fixed and the zip of OrthoInspector v1.40 is updated in the download section.

A bug generated duplicated entries for many-to-one and many-to-many relations in CSV and TSV output formats, only for the Orthoinspector command-line. The bug is now fixed and the zip of OrthoInspector v1.40 is updated in the download section.

Queries with blast search generated critical errors,  when only 1 sequence was used for the blast. The bug is corrected and the zip archive of version 1.31 is updated.

ORTHOINSPECTOR V1.31 is available for download. Here are the main changes:

+ a new graph layout, best-hit density graph, is available. It is now the default displayed graph. This graph cannot be displayed if the Blast data tables were not created during the installation process.
* correction of a bug in the graphical interface. The use of a fasta file as a query crashed the application if some special characters were used.
* query blast searches are now faster

ORTHOINSPECTOR V1.30 is available for download. Here are the main changes:

+ the graphical interface and the 2 command-line binaries share the same ./lib directory.

+ if OrthoInspector is connected to an empty database, it automatically creates the orthoinspector database schema (MySQL & PostgreSQL only).

- previous 'direct' mode of data insertion is abandonned.

+ 'direct' mode is replaced by temporary database dumps that are written in a selected directory and are directly transfered to the database. Update  operations are now really faster. This mode is currently only compatible with MySQL and PostgreSQL. For other database engines, first you need to
create the OrthoInspector schema in your database, second transfer manually the table dumps with your own SQL queries.

+ rename the 'direct' and 'dumps' options in the installation command-line to 'direct_insertion' and 'dumps_only'

+ installation steps are more verbose in the graphical interface by adding new progress bars.

+ errors occuring during the installation process are better handled.

+ during the blast parsing step of the installation process, the user can choose to produce (or not) blast and noHit table data. These data are no longer compulsory for orthology inference. Here are the consequences if you avoid to produce these data:

• no blast data: vastly reduce the database size. Blastoutputs cannot be browsed in the graphical interface.
• no nohit data: the 'statistics' tool of the graphical interface will produce less statistics about sequences without blast hits.

To propose these options, a new menu has been implemented in the graphical interface and 2 new options exists in the installation command-line.

+ A graphical bug is corrected in the presence/absence tool of the graphical interface.

+ A bug was introduce in version 1.21 for the presence/absence tool, it produced incomplete results files. This has been corrected.

+ Inclusive/exlusive modes have been renamed 'between all possible organism pairs' / 'between base organism pairs'.

+ a simple FASTA output format has been added in the client command-line. These files can be directly loaded in multiple alignement programs.

+ several other minor bugfix

During the OrthoInspector command-line installation, depending on the server localisation configuration, some dates format variations (2011-01-01, 01-01-2011...)  caused errors. Moreover some dates were in the YYYY/MM/DD format in the benchmark.

These issues have been corrected. The binaries and the organism.xml file of the benchmark are updated in the Downloads section.

Changes :

+  Session systems to save/load analysis sessions. Sessions are saved in files with the *.ois (orthoinspecor session) extension.

+   Results are now displayed in a table, new queries using previous can be launched.

+   Pressence/absence tools now includes 2 algorithms : inclusive and exclusive.

# Inclusive algorithm : use non-absolute intersection of the criteria

ex : we want human proteins that have orthologs in mouse but not in rat.
human<->rat orthology is verified and must be rejected.
human<->mouse orthology is verified and must be validated.
rat<->mouse orthology is not verified.

# Exclusive algorithm : use absolute intersection of the criteria

ex : we want human proteins that have orthologs in mouse but not in rat.
human<->rat orthology is verified and must be rejected.
human<->mouse orthology is verified and must be validated.
rat<->mouse orthology is verified and if one protein previously considered absent in rat and present in mouse show some rat<->mouse orthology, is it not  considered as corresponding to wanted criteria.

+   Administrators can now hide the 'installation menu' by modifying the 'menu.installation' property in the 'GeneralProperties.properties' file.

*    All database schema upper-case letters are know removed, for a best MySQL compatibility (MySQL naming is case-sensitive). Users of previous versions must set all tables/columns to lower case in their database. All files of the orthoinspector website are updated in this way (schema, scripts...).

*    Minor bug fix in the command-line for installation.

The previous file describing  the MySQL database schema was leading to the following error on some configurations :

ERROR 1061 (42000) at line 420: Duplicate key name 'oto_orgaa_fk_constraint'

This is now fixed, you can download the corrected file in the 'Download' section.

ORTHOINSPECTOR V1.1 is available.

Changes :

+ Refactoring of the project packages

+ Fasta outputs in presence/absence bilan

* Correction of a bug that restricted databases access

* Multiple minor bug fix

Graphical Interface updated to  v 1.11. Only the graphical interface archive is modified.

* Correction of a bug in the presence/absence bilan that included organisms not asked by the user in the results.

* Modification of the CSV output format (presence/absence  bilan)  for best readability.

Welcome to the OrthoInspector project website !

What is OrthoInspector ?

OrthoInspector is a new software system for orthology/paralogy analysis. It is made available as an independent software suite that can be downloaded and installed for local use. Its purpose is to facilitate the installation and the maintenance of a database describing orthology/inparalogy relations and to provide tools to exploit these data.

What can OrthoInspector do ?

The suite is separated in two parts : a command-line software and a graphical interface. Command line querying facilitates the integration of the software in high throughput processing pipelines and a graphical interface provides easy, intuitive access to results for the non-expert. Moreover the graphical interface provides extended tools to visualize the produced data.

What are the requirements ?

OrthoInspector is compatible with all systems supporting Java 1.6.x JVM. Its database schema is compatible with any relational database engine supported by a JDBC driver.

Any restrictions ?

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 ! ;-)