Index of /download/homology/orthologs/A_oryzae_RIB40_S_pombe_by_inparanoid

 Name                                                  Last modified      Size  Description
 Parent Directory                                                           -   
 A_oryzae_RIB40_S_pombe_orthologs.txt                  15-Mar-2012 13:52   94K  
 inparanoid_output.03-15-2012.txt                      15-Mar-2012 13:52  1.3M  
 orf_trans_all_Aspergillus_oryzae.03-15-2012.fasta.gz  15-Mar-2012 13:52  3.9M  
 orf_trans_all_Saccharomyces_pombe.03-15-2012.fasta.gz 15-Mar-2012 13:52  1.5M  
 rejected_sequences.wormpep.03-15-2012.fasta.gz        15-Mar-2012 13:52  1.7K  
 wormpep.03-15-2012.fasta.gz                           15-Mar-2012 13:52  5.4M  

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

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 from AspGD
were compared to the latest set of S. pombe proteins from the Sanger Institute; the set 
of C. elegans 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_pombe_orthologs.txt                       - the processed output, with the A. oryzae RIB40 
			                                     gene name, the Systematic name, and the gene name from PomBase

orf_trans_all_A_oryzae.MM-DD-YYYY.fasta.gz                 - the A. oryzae RIB40 protein file used as input
orf_trans_all_Saccharomyces_pombe.MM-DD-YYYY.fasta.gz      - the S. pombe protein complement
wormpep.MM-DD-YYYY.fasta.gz                                - the C. elegans protein set used as an outgroup

inparanoid_output.MM-DD-YYYY.txt                           - the raw output from InParanoid
rejected_sequences.wormpep.MM-DD-YYYY.fasta.gz             - the sequences rejected due to the C. elegans 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.