Index of /download/homology/orthologs/A_oryzae_RIB40_S_cerevisiae_by_inparanoid

 Name                                                 Last modified      Size  Description
 Parent Directory                                                          -   
 A_oryzae_RIB40_S_cerevisiae_orthologs.txt            15-Mar-2012 08:44   58K  
 inparanoid_output.03-15-2012.txt                     15-Mar-2012 08:44  919K  
 orf_trans_all_Aspergillus_oryzae.03-15-2012.fasta.gz 15-Mar-2012 08:44  3.9M  
 orf_trans_all_Saccharomyces.03-15-2012.fasta.gz      15-Mar-2012 08:44  2.4M  
 pompep.03-15-2012.fasta.gz                           15-Mar-2012 08:44  1.5M  
 rejected_sequences.pompep.03-15-2012.fasta.gz        15-Mar-2012 08:44   27K  

This directory contains the orthology assignments between A. oryzae RIB40 
and S. cerevisiae.  

The assignments were made using InParanoid version 3.0 (http://inparanoid.sbc.su.se/).

To run InParanoid, the current set of A. oryzae RIB40 protein sequences originally 
downloaded from the Broad Institute Aspergillus download page on 23-Feb-2009, were compared
to the latest set of S. cerevisiae proteins from SGD as of 08-20-2011; the set 
of S. pombe proteins from the Sanger Institute was used as an outgroup.
Stringent cutoffs were set: BLOSUM80 (instead of the default BLOSUM62),
and an InParanoid score of 100%. 

Please note, the ortholog pairings were automatically generated, with no
curator intervention.  Thus, there will occasionally be pairings that
may not occur with a different scoring matrix.  In the interests of
automating the process, we do not intend to hand-curate the ortholog
pairs at this time.


Files are provided containing the input sequences that were used by InParanoid, 
and the raw  output file that was generated by  InParanoid.  In addition,
a file containing the processed output, listing orthology assigments
is also provided.


The following files are available:

A_oryzae_RIB40_S_cerevisiae_orthologs.txt     - the processed output, with the A. oryzae RIB40 
			                                     gene name, the SGDID, and the gene/ORF name from SGD

pompep.MM-DD-YYYY.fasta.gz                         - the S. pombe protein set used as an outgroup

inparanoid_output.MM-DD-YYYY.txt                    - the raw output from InParanoid
rejected_sequences.pompep.MM-DD-YYYY.fasta.gz       - the sequences rejected due to the S. pombe outgroup



The dates (indicated by MM-DD-YYYY) in the above file names represent the date when 
the input files were downloaded and latest set of ortholog predictions generated.