Index of /download/homology/orthologs/A_oryzae_RIB40_S_cerevisiae_by_inparanoid

Icon  Name                                                 Last modified      Size  Description
[DIR] Parent Directory - [TXT] A_oryzae_RIB40_S_cerevisiae_orthologs.txt 23-Jan-2017 21:11 105K [TXT] inparanoid_output.01-23-2017.txt 23-Jan-2017 21:11 954K [   ] orf_trans_all_Aspergillus_oryzae.01-23-2017.fasta.gz 23-Jan-2017 21:11 4.2M [   ] orf_trans_all_Saccharomyces.01-23-2017.fasta.gz 23-Jan-2017 21:11 2.5M [   ] pompep.01-23-2017.fasta.gz 23-Jan-2017 21:11 1.5M [   ] rejected_sequences.pompep.01-23-2017.fasta.gz 23-Jan-2017 21:11 35K
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 from AspGD were
compared to the latest set of S. cerevisiae proteins from SGD; 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 ORF name,
			                               A. oryzae gene name, A. oryzae AspGDID, SGD ORF name,
						       SGD gene name, and SGDID.

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

orf_trans_all_Saccharomyces.MM-DD-YYYY.fasta.gz      - the S. cerevisiae protein file used as input

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.