Index of /download/homology/orthologs/A_oryzae_RIB40_S_pombe_by_inparanoid

Icon  Name                                                        Last modified      Size  Description
[DIR] Parent Directory - [TXT] A_oryzae_RIB40_S_pombe_orthologs.txt 24-Jan-2017 04:14 173K [TXT] inparanoid_output.01-24-2017.txt 24-Jan-2017 04:14 1.3M [   ] orf_trans_all_Aspergillus_oryzae.01-24-2017.fasta.gz 24-Jan-2017 04:14 4.2M [   ] orf_trans_all_Saccharomyces_pombe.05-24-2012.fasta.gz 24-May-2012 11:53 1.5M [   ] orf_trans_all_Schizosaccharomyces_pombe.09-16-2013.fasta.gz 17-Sep-2013 00:42 1.5M [   ] pompep.01-24-2017.fasta.gz 24-Jan-2017 04:14 1.4M [   ] rejected_sequences.wormpep.01-24-2017.fasta.gz 24-Jan-2017 04:14 1.5K [   ] wormpep.01-24-2017.fasta.gz 24-Jan-2017 04:14 5.1M
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 ORF name,
			                                      A. oryzae gene name, A. oryzae AspGDID, PomBase Systematic name, PomBase gene name.

orf_trans_all_A_oryzae.MM-DD-YYYY.fasta.gz                  - the A. oryzae RIB40 protein file used as input
orf_trans_all_Schizosaccharomyces_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.