Index of /download/homology/orthologs/A_fumigatus_Af293_S_cerevisiae_by_inparanoid

Icon  Name                                                    Last modified      Size  Description
[DIR] Parent Directory - [TXT] A_fumigatus_Af293_S_cerevisiae_orthologs.txt 23-Jan-2017 18:32 102K [   ] all_A_fumigatus_Af293_proteins.10-03-2012.fasta.gz 30-Sep-2012 08:58 3.5M [TXT] inparanoid_output.01-23-2017.txt 23-Jan-2017 18:32 1.0M [TXT] inparanoid_output.10-03-2012.txt 03-Oct-2012 15:53 963K [   ] orf_trans_all_Aspergillus_fumigatus.01-23-2017.fasta.gz 23-Jan-2017 18:32 3.6M [   ] orf_trans_all_Saccharomyces.01-23-2017.fasta.gz 23-Jan-2017 18:32 2.5M [   ] orf_trans_all_Saccharomyces.10-03-2012.fasta.gz 03-Feb-2011 00:00 2.4M [   ] pompep.01-23-2017.fasta.gz 23-Jan-2017 18:32 1.5M [   ] pompep.10-03-2012.fasta.gz 03-Oct-2012 14:53 1.5M [   ] rejected_sequences.pompep.01-23-2017.fasta.gz 23-Jan-2017 18:32 36K [   ] rejected_sequences.pompep.10-03-2012.fasta.gz 03-Oct-2012 15:48 28K
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 AspGD
were compared to the latest set of S. cerevisiae proteins from SGD; 
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 ORF name,
			                                  gene name, A. fumigatus AspGDID, SGD ORF name, SGD gene name, and SGDID.

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

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 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.