Index of /download/homology/orthologs/A_oryzae_RIB40_C_albicans_by_inparanoid

Icon  Name                                                 Last modified      Size  Description
[DIR] Parent Directory - [TXT] A_oryzae_RIB40_C_albicans_orthologs.txt 24-Jan-2017 09:45 147K [TXT] inparanoid_output.01-24-2017.txt 24-Jan-2017 09:45 1.1M [   ] orf_trans_all_Aspergillus_oryzae.01-24-2017.fasta.gz 24-Jan-2017 09:45 4.2M [   ] orf_trans_all_Candida_albicans.01-24-2017.fasta.gz 24-Jan-2017 09:45 2.3M [   ] pompep.01-24-2017.fasta.gz 24-Jan-2017 09:45 1.5M [   ] rejected_sequences.pompep.01-24-2017.fasta.gz 24-Jan-2017 09:45 32K
This directory contains the orthology assignments between A. oryzae RIB40 and C. albicans.

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 C. albicans proteins from the Candida Genome Database (CGD); 
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_C_albicans_orthologs.txt                        - the processed output.
							       The format of the pairwise ortholog and Best Hit files (updated
							       September 2012) contains three tab-delimited columns for each
							       organism.
							       For each organism, the columns display:
							       - the systematic name of the gene
							       - the standard/genetic name of the gene (if one exists)
							       - the database identifier for the gene.

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