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 25-Jan-2017 15:33 75K [TXT] A_fumigatus_Af293_A_niger_CBS_513_88_best_hits.txt 25-Jan-2017 15:35 98K [TXT] A_fumigatus_Af293_A_oryzae_RIB40_best_hits.txt 25-Jan-2017 15:36 112K [TXT] A_fumigatus_Af293_C_albicans_best_hits.txt 25-Jan-2017 15:42 190K [TXT] A_fumigatus_Af293_N_crassa_best_hits.txt 25-Jan-2017 15:44 151K [TXT] A_fumigatus_Af293_S_cerevisiae_best_hits.txt 25-Jan-2017 15:32 158K [TXT] A_fumigatus_Af293_S_pombe_best_hits.txt 25-Jan-2017 15:39 137K [TXT] A_nidulans_FGSC_A4_A_fumigatus_Af293_best_hits.txt 25-Jan-2017 15:15 105K [TXT] A_nidulans_FGSC_A4_A_niger_CBS_513_88_best_hits.txt 25-Jan-2017 15:18 114K [TXT] A_nidulans_FGSC_A4_A_oryzae_RIB40_best_hits.txt 25-Jan-2017 15:20 133K [TXT] A_nidulans_FGSC_A4_C_albicans_best_hits.txt 25-Jan-2017 15:26 196K [TXT] A_nidulans_FGSC_A4_N_crassa_best_hits.txt 25-Jan-2017 15:29 174K [TXT] A_nidulans_FGSC_A4_S_cerevisiae_best_hits.txt 25-Jan-2017 15:14 160K [TXT] A_nidulans_FGSC_A4_S_pombe_best_hits.txt 25-Jan-2017 15:22 144K [TXT] A_niger_CBS_513_88_A_fumigatus_Af293_best_hits.txt 25-Jan-2017 15:51 150K [TXT] A_niger_CBS_513_88_A_nidulans_FGSC_A4_best_hits.txt 25-Jan-2017 15:53 129K [TXT] A_niger_CBS_513_88_A_oryzae_RIB40_best_hits.txt 25-Jan-2017 15:57 173K [TXT] A_niger_CBS_513_88_C_albicans_best_hits.txt 25-Jan-2017 16:03 231K [TXT] A_niger_CBS_513_88_N_crassa_best_hits.txt 25-Jan-2017 16:08 234K [TXT] A_niger_CBS_513_88_S_cerevisiae_best_hits.txt 25-Jan-2017 15:48 192K [TXT] A_niger_CBS_513_88_S_pombe_best_hits.txt 25-Jan-2017 16:00 174K [TXT] A_oryzae_RIB40_A_fumigatus_Af293_best_hits.txt 25-Jan-2017 16:14 198K [TXT] A_oryzae_RIB40_A_nidulans_FGSC_A4_best_hits.txt 25-Jan-2017 16:17 174K [TXT] A_oryzae_RIB40_A_niger_CBS_513_88_best_hits.txt 25-Jan-2017 16:20 207K [TXT] A_oryzae_RIB40_C_albicans_best_hits.txt 25-Jan-2017 16:26 262K [TXT] A_oryzae_RIB40_N_crassa_best_hits.txt 25-Jan-2017 16:30 262K [TXT] A_oryzae_RIB40_S_cerevisiae_best_hits.txt 25-Jan-2017 16:11 215K [TXT] A_oryzae_RIB40_S_pombe_best_hits.txt 25-Jan-2017 16:22 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.