Index of /download/homology/orthologs/A_fumigatus_Af293_S_cerevisiae_by_inparanoid

 Name                                               Last modified      Size  Description
 Parent Directory                                                        -   
 A_fumigatus_Af293_S_cerevisiae_orthologs.txt       04-Feb-2010 21:21   73K  
 all_A_fumigatus_Af293_proteins.09-21-2009.fasta.gz 23-Sep-2009 16:13  2.9M  GZIP compressed docume>
 inparanoid_output.09-21-2009.txt                   23-Sep-2009 16:13  1.5M  
 orf_trans_all_Saccharomyces.09-21-2009.fasta.gz    23-Sep-2009 16:13  2.4M  GZIP compressed docume>
 rejected_sequences.wormpep.09-21-2009.fasta.gz     23-Sep-2009 16:13  4.3K  GZIP compressed docume>
 wormpep.09-21-2009.fasta.gz                        23-Sep-2009 16:13  5.3M  GZIP compressed docume>

This directory contains the orthology assignments between A. fumigatus Af293
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. fumigatus Af293 protein sequences from the 
Broad Institute (http://www.broad.mit.edu/annotation/genome/aspergillus_group/MultiDownloads.html, 
originally obtained on 23-Feb-2009 and downloaded from 
http://aspgd.igs.umaryland.edu/cgi-bin/asp2_v2/shared/show_organism.cgi?site=asp2_v2&id=8
on 09-21-2009) were compared to the latest set of S. cerevisiae proteins from SGD as of 09-21-2009; 
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_fumigatus_Af293_S_cerevisiae_orthologs.txt            - the processed output, with the A. fumigatus Af293
			                                  gene name, the SGDID, and the gene/ORF name from SGD

all_A_fumigatus_Af293_proteins.MM-DD-YYYY.fasta.gz      - the A. fumigatus Af293 protein file used as input
orf_trans_all_Saccharomyces.MM-DD-YYYY.fasta.gz         - the S. cerevisiae protein file used as input
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 worm 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.