Index of /download/homology/orthologs

Icon  Name                                                         Last modified      Size  Description
[DIR] Parent Directory                                                                  -   
[DIR] A_fumigatus_Af293_A_nidulans_FGSC_A4_by_Jaccard_clustering/  31-Jan-2012 19:11    -   
[DIR] A_fumigatus_Af293_A_niger_CBS_513_88_by_Jaccard_clustering/  31-Jan-2012 19:11    -   
[DIR] A_fumigatus_Af293_A_oryzae_RIB40_by_Jaccard_clustering/      31-Jan-2012 19:11    -   
[DIR] A_fumigatus_Af293_S_cerevisiae_by_inparanoid/                31-Jan-2012 19:11    -   
[DIR] A_fumigatus_Af293_S_pombe_by_inparanoid/                     01-Feb-2012 04:57    -   
[DIR] A_nidulans_FGSC_A4_A_fumigatus_Af293_by_Jaccard_clustering/  31-Jan-2012 19:11    -   
[DIR] A_nidulans_FGSC_A4_A_niger_CBS_513_88_by_Jaccard_clustering/ 31-Jan-2012 19:11    -   
[DIR] A_nidulans_FGSC_A4_A_oryzae_RIB40_by_Jaccard_clustering/     31-Jan-2012 19:11    -   
[DIR] A_nidulans_FGSC_A4_S_cerevisiae_by_inparanoid/               31-Jan-2012 19:11    -   
[DIR] A_nidulans_FGSC_A4_S_pombe_by_inparanoid/                    01-Feb-2012 05:45    -   
[DIR] A_niger_CBS_513_88_A_fumigatus_Af293_by_Jaccard_clustering/  31-Jan-2012 19:11    -   
[DIR] A_niger_CBS_513_88_A_nidulans_FGSC_A4_by_Jaccard_clustering/ 31-Jan-2012 19:11    -   
[DIR] A_niger_CBS_513_88_A_oryzae_RIB40_by_Jaccard_clustering/     31-Jan-2012 19:11    -   
[DIR] A_niger_CBS_513_88_S_cerevisiae_by_inparanoid/               31-Jan-2012 19:11    -   
[DIR] A_niger_CBS_513_88_S_pombe_by_inparanoid/                    03-Feb-2012 05:41    -   
[DIR] A_oryzae_RIB40_A_fumigatus_Af293_by_Jaccard_clustering/      31-Jan-2012 19:11    -   
[DIR] A_oryzae_RIB40_A_nidulans_FGSC_A4_by_Jaccard_clustering/     31-Jan-2012 19:11    -   
[DIR] A_oryzae_RIB40_A_niger_CBS_513_88_by_Jaccard_clustering/     31-Jan-2012 19:11    -   
[DIR] A_oryzae_RIB40_S_cerevisiae_by_inparanoid/                   31-Jan-2012 19:11    -   
[DIR] A_oryzae_RIB40_S_pombe_by_inparanoid/                        04-Feb-2012 05:16    -   

This directory contains data pertaining to orthology assignments among
various Aspergillus species/strains, and between Asprgillus species
and other organisms.

The name of the individual subdirectories lists the species compared.

Pairwise ortholog mappings to S. cerevisiae were generated using the
InParanoid software developed at the Karolinska Institutet
(http://inparanoid.sbc.su.se/). InParanoid comparisons use the latest
set of S. cerevisiae proteins from SGD; 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%. FIles are provided containing the input
sequences that were used and the raw output files that were generated
by InParanoid.  In addition, files containing the processed output,
listing the orthology assignments, are provided.

Ortholog assignments among the Aspergillus species in AspGD were made
using a Jaccard clustering approach. The clustering is a two step
process, with the first step clustering proteins within each
genome/strain (using the results of an all-vs-all BLASTP search with
an 80% BLASTP percent identity threshold and an e-value threshold of
1e-5, and a minimum Jaccard similarity coefficient of 0.6). The
clusters that are generated by the first step are referred to as
simply "Jaccard clusters" and these clusters are themselves clustered
in the second step, using a reciprocal best BLAST match linkage, to
create the Jaccard Orthologous Clusters. The sets of clusters were
built from an initial cluster analysis with a minimum percent coverage
score of 80% (step 1) and a reciprocal best hit analysis with a
minimum percent coverage score of 80% (step 2). Note, that the
ortholog assignments 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.