Index of /download/inparanoid

 Name                    Last modified      Size  Description
 Parent Directory                             -   
 CA_SC_orthologs.txt     01-Sep-2005 16:11   90K  
 inparanoid_output.txt   01-Sep-2005 16:11  1.1M  
 orf_trans_all_Candid..> 01-Sep-2005 16:11  3.1M  
 orf_trans_all_Saccha..> 01-Sep-2005 16:11  3.5M  
 rejected_sequences.w..> 01-Sep-2005 16:11  3.9K  
 wormpep145.fasta        01-Sep-2005 16:11   12M  

This directory contains the input sequences that were used to
determine orthology assignments between C. albicans and S. cerevisiae,
using InParanoid (http://inparanoid.cgb.ki.se/) and the output file
that was generated from InParanoid.  In addition, a file containing
the processed output, listing orthology assigments is also provided.

To run InParanoid, the haploid complement of C. albicans proteins from
CGD was compared to the latest set of S. cerevisiae proteins from SGD
(as of August 10th, 2005), and the set of C. elegans proteins from the
Sanger Institute, in wormpep 145, was used as an outgroup. Stringent
cutoffs were set: BLOSUM80 (instead of the default BLOSUM62), and an
InParanoid score of 100%.  In total, 3594 ortholog mappings met these
criteria.

The following files are available:

orf_trans_all_Candida_haploid.fasta - the C. albicans haploid protein complement
orf_trans_all_Saccharomyces.fasta   - the S. cerevisiae protein complement
wormpep145.fasta                    - the C. elegans protein set used as an outgroup
inparanoid_output.txt               - the raw output from InParanoid
rejected_sequences.wormpep.fasta    - the sequences rejected due to the worm outgroup
CA_SC_orthologs.txt                 - the processed output, with the orf19 id, the SGDID, and the gene/ORF name from SGD