Index of /download/homology/orthologs/A_nidulans_FGSC_A4_N_crassa_by_inparanoid
Name Last modified Size Description
Parent Directory -
A_nidulans_FGSC_A4_N_crassa_orthologs.txt 24-Jan-2017 12:08 300K
Neurospora_crassa_proteins.01-24-2017.fasta.gz 24-Jan-2017 12:08 3.0M
inparanoid_output.01-24-2017.txt 24-Jan-2017 12:08 2.5M
orf_trans_all_Aspergillus_nidulans.01-24-2017.fasta.gz 24-Jan-2017 12:08 3.9M
pompep.01-24-2017.fasta.gz 24-Jan-2017 12:08 1.5M
rejected_sequences.pompep.01-24-2017.fasta.gz 24-Jan-2017 12:08 2.9K
This directory contains the orthology assignments between A. nidulans FGSC A4 and Neurospora crassa.
The assignments were made using InParanoid version 3.0 (http://inparanoid.sbc.su.se/).
To run InParanoid, the current set of A. nidulans FGSC A4 protein sequences from AspGD
were compared to the latest set of Neurospora proteins from the Broad institute;
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%.
Please note, 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.
Files are provided containing the input sequences that were used by InParanoid,
and the raw output file that was generated by InParanoid. In addition,
a file containing the processed output, listing orthology assigments
is also provided.
The following files are available:
A_nidulans_FGSC_A4_N_crassa_orthologs.txt - the processed output.
The format of the pairwise ortholog and Best Hit files (updated
September 2012) contains three tab-delimited columns for each
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.
orf_trans_all_A_nidulans.MM-DD-YYYY.fasta.gz - the A. nidulans FGSC A4 protein file used as input
Neurospora_crassa_proteins.MM-DD-YYYY.fasta.gz - the N. crassa protein file used as input
pompep.MM-DD-YYYY.fasta.gz - the S. pombe protein set used as an outgroup
inparanoid_output.MM-DD-YYYY.txt - the raw output from InParanoid
rejected_sequences.pompep.MM-DD-YYYY.fasta.gz - the sequences rejected due to the S. pombe outgroup
The dates (indicated by MM-DD-YYYY) in the above file names represent the date when
the input files were downloaded and latest set of ortholog predictions generated.