This directory contains the input sequences that were used to
determine orthology assignments between C. albicans Assembly 21 and
S. cerevisiae, using InParanoid version 3.0
(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 April 7th 2008), and the set of C. elegans proteins from the
Sanger Institute, in wormpep 188, was used as an outgroup. Stringent
cutoffs were set: BLOSUM80 (instead of the default BLOSUM62), and an
InParanoid score of 100%.  In total, 3453 ortholog mappings met these
criteria.  BLAST version 2.2.18 was used by InParanoid.

Note, that 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.

Please also note that, in the Assembly 21-based mapping, orthologs are
not computed or displayed for the C. albcans ORFs that were present in
a prior Assembly 19 and subsequently deleted from Assembly 21. The
orthologs of these ORFs are present in the Assembly 19-based mapping file.

For C. albicans proteins that did not have an ortholog that meets
these criteria, we used BLASTp, using the same parameters as were used
by InParanoid (-F \"m S\" -M BLOSUM80) with an expectation value (E)
of 1e-5 to identify their best hit in the S. cerevisiae protein
complement.  Best hits were identified for 1373 of the C. albicans
proteins.  These data are available in the same format as the ortholog
data.


The following files are available:

orf_trans_all_Candida_Assembly_21_haploid.fasta.gz - the C. albicans haploid protein complement
orf_trans_all_Saccharomyces.fasta.gz               - the S. cerevisiae protein complement
wormpep188.fasta.gz                                - the C. elegans protein set used as an outgroup
inparanoid_output.txt                              - the raw output from InParanoid
rejected_sequences.wormpep.fasta.gz                - 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
best_hits.txt                                      - best hits (expectation value of 1e-5) for proteins without orthologs