Updates

OrthoInspector v3.0: MySQLite installation available (09/2018):

  • SQLite database support for easier installation. We recommend using it for small databases.
  • Code optimization.
  • Change to a data structure more adapted to high volume of data. (Fastutil library Hashmap)

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.

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:

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

All:

  • Several minor bugs corrections

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

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

All: * Several minor bugs corrections

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

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

All: * 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)

Command-line: + 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.

All: * 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.