Index of /download/homology/orthologs

Icon  Name                                       Last modified      Size  Description
[DIR] Parent Directory                                                -   
[DIR] C_albicans_SC5314_C_glabrata_CBS138/       27-Jan-2012 08:30    -   
[DIR] C_albicans_SC5314_S_cerevisiae/            27-Jan-2012 08:30    -   
[DIR] C_glabrata_CBS138_C_albicans_SC5314/       27-Jan-2012 08:30    -   
[DIR] C_glabrata_CBS138_S_cerevisiae/            27-Jan-2012 08:30    -   
[TXT] Calb_Cdub_positional_orthologs_Assem20.txt 04-Aug-2008 14:04  121K  

This directory contains data pertaining to orthology assignments
between C. albicans and other organisms.

The ortholog mappings are made by pairwise species comparisons using
the InParanoid (http://inparanoid.sbc.su.se/cgi-bin/index.cgi)
software, developed at the Karolinska Institutet, as follows:

C. albicans SC5314 Assembly 21 (haploid protein complement) against
S. cerevisiae
C. glabrata CBS138 against S. cerevisiae 
C. glabrata CBS138 against C. albicans SC5314 Assembly 21
C. albicans SC5314 Assembly 21 against C. glabrata CBS138

Please note: Analysis conducted June 2011 determined that there is no
effect of directionality on the mapping C. albicans against
C. glabrata, that is, the two mappings are identical, and C. glabrata
CBS138 against C. albicans SC5314 Assembly 21 yields the same result
as C. albicans SC5314 Assembly 21 against C. glabrata CBS138.

Comparisons are made on approximately four times a year.  The latest
set of S. cerevisiae proteins is obtained from the
Saccharomyces Genome Database (SGD), and the set of S. pombe
proteins from the Sanger Institute is used as an outgroup.  Stringent
cutoffs are set: BLOSUM80 (instead of the default BLOSUM62), and an
InParanoid score of 100% (parameters: -F \"m S\" -M BLOSUM80). Note,
that the ortholog pairings are automatically generated, with no
curator intervention. Thus, there will occasionally be pairings that
may not occur with a different scoring matrix. In the interest of
automating the process, we do not intend to hand-curate the ortholog
pairs at this time. Please also note that orthologs are not computed
or displayed for ORFs that were present in a previous version of the
reference annotation, but which are designated as "deleted" in the
current set.

For proteins that do not have an ortholog (in a given species) that
meets the strict criteria we use to define orthology, we use BLASTp
(with parameters -F \"m S\" -M BLOSUM80), with an expectation value
(E) of 1e-5, to identify a best hit in the protein complement.

This directory contains subdirectories with information about
individual pairwise mappings.


----------------------------

These ortholog mappings between C. albicans and C. dubliniensis were
provided to CGD by John Gamble and Matthew Berriman at the Wellcome
Trust Sanger Institute (http://www.sanger.ac.uk/). The C. dubliniensis
orthologs are manually curated positional orthologs based on synteny.

Please note: This is a static file that is not updated.  Mappings were
based on C. albicans Assembly 20.