Index of /download/homology/best_hits

Icon  Name                                                Last modified      Size  Description
[DIR] Parent Directory - [TXT] A_fumigatus_Af293_A_nidulans_FGSC_A4_best_hits.txt 01-Sep-2015 16:26 75K [TXT] A_fumigatus_Af293_A_niger_CBS_513_88_best_hits.txt 01-Sep-2015 16:27 98K [TXT] A_fumigatus_Af293_A_oryzae_RIB40_best_hits.txt 01-Sep-2015 16:29 112K [TXT] A_fumigatus_Af293_C_albicans_best_hits.txt 09-Sep-2015 00:22 190K [TXT] A_fumigatus_Af293_N_crassa_best_hits.txt 01-Sep-2015 16:37 151K [TXT] A_fumigatus_Af293_S_cerevisiae_best_hits.txt 01-Sep-2015 16:24 158K [TXT] A_fumigatus_Af293_S_pombe_best_hits.txt 01-Sep-2015 16:31 137K [TXT] A_nidulans_FGSC_A4_A_fumigatus_Af293_best_hits.txt 01-Sep-2015 16:08 105K [TXT] A_nidulans_FGSC_A4_A_niger_CBS_513_88_best_hits.txt 01-Sep-2015 16:10 114K [TXT] A_nidulans_FGSC_A4_A_oryzae_RIB40_best_hits.txt 01-Sep-2015 16:13 133K [TXT] A_nidulans_FGSC_A4_C_albicans_best_hits.txt 08-Sep-2015 23:23 196K [TXT] A_nidulans_FGSC_A4_N_crassa_best_hits.txt 01-Sep-2015 16:21 174K [TXT] A_nidulans_FGSC_A4_S_cerevisiae_best_hits.txt 01-Sep-2015 16:07 160K [TXT] A_nidulans_FGSC_A4_S_pombe_best_hits.txt 01-Sep-2015 16:15 144K [TXT] A_niger_CBS_513_88_A_fumigatus_Af293_best_hits.txt 01-Sep-2015 16:43 150K [TXT] A_niger_CBS_513_88_A_nidulans_FGSC_A4_best_hits.txt 01-Sep-2015 16:46 129K [TXT] A_niger_CBS_513_88_A_oryzae_RIB40_best_hits.txt 01-Sep-2015 16:49 173K [TXT] A_niger_CBS_513_88_C_albicans_best_hits.txt 09-Sep-2015 01:23 231K [TXT] A_niger_CBS_513_88_N_crassa_best_hits.txt 01-Sep-2015 17:00 234K [TXT] A_niger_CBS_513_88_S_cerevisiae_best_hits.txt 01-Sep-2015 16:40 192K [TXT] A_niger_CBS_513_88_S_pombe_best_hits.txt 01-Sep-2015 16:52 175K [TXT] A_oryzae_RIB40_A_fumigatus_Af293_best_hits.txt 01-Sep-2015 17:06 198K [TXT] A_oryzae_RIB40_A_nidulans_FGSC_A4_best_hits.txt 01-Sep-2015 17:09 174K [TXT] A_oryzae_RIB40_A_niger_CBS_513_88_best_hits.txt 01-Sep-2015 17:12 207K [TXT] A_oryzae_RIB40_C_albicans_best_hits.txt 09-Sep-2015 02:23 262K [TXT] A_oryzae_RIB40_N_crassa_best_hits.txt 01-Sep-2015 17:23 262K [TXT] A_oryzae_RIB40_S_cerevisiae_best_hits.txt 01-Sep-2015 17:04 215K [TXT] A_oryzae_RIB40_S_pombe_best_hits.txt 01-Sep-2015 17:15 198K
To determine orthology assignments among Aspergillus species, we used a
Jaccard clustering approach; to determine between Aspergillus species and S. cerevisiae, 
we used InParanoid (http://inparanoid.sbc.su.se/), described in detail at 
http://www.aspgd.org/download/homology/orthologs/.
 
For proteins that did not have an ortholog (in a given species) that meets
the strict criteria we use to define orthology, 
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 the best hit in the protein complement.  

These best hits data are available in the same format as the files containing
the ortholog data, with 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 

The ortholog files are available at
http://www.aspgd.org/download/homology/orthologs/

The best hits data are updated quaterly to ensure that the predictions 
are based on the most up-to-date information.