INPARANOID: Eukaryotic Ortholog Groups
Release 6.0


1. Introduction

InParanoid is a program for automatic identification of orthologs
while differentiating between inparalogs and outparalogs. An
InParanoid cluster is seeded by a reciprocally bestmatching ortholog
pair, around which inparalogs are gathered independently, while
outparalogs are excluded.  The InParanoid database is a collection of
pairwise ortholog groups aiming to include all 'completely sequenced'
eukaryotic genomes. By this we mean above 6X coverage, and less than
1% X letters in the protein sequences.


2. Online access

The InParanoid eukaryotic ortholog database is available both for
direct online access as well as for downloading. Online the user has
the option to view all clusters between two species, search for
clusters based on gene ID or free text search, as well as doing a
blast search based on a sequence.  Online access is available at
http://inparanoid.sbc.su.se.


3. Downloadable content

The current database is available for dowload at
http://inparanoid.sbc.su.se/download/current.

All two-species comparisons are available as HTML, XML, SQL and raw
text files. Both the original and the processed (non-redundant)
sequences used for analysis are available as fasta files. Included
with the XML files is a RELAX NG schema file called InParanoid.rng,
this can be used to validate the xml files using xmllint:

xmllint --noout  --relaxng InParanoid.rng fileToValidate.xml

It is also possible to download previous versions at
http://inparanoid.sbc.su.se/download/old_versions.


4. Stand alone program

InParanoid Version 2.0 is available - email inparanoid@sbc.su.se to
obtain a copy.


5. Database statistics

Version	Date	Species		Species_pairs	Ortholog_groups	Inparalogs
2.0	05/03	7		21		57611		239690
3.0	04/05	7		21		60687		262777
4.0	04/05	17		136		559269		1590053
5.1	01/07	26		325		1501438		4625369
6.0	09/07	35		595		2642187		7240640