Index of /download/homology/orthologs/C_glabrata_CBS138_S_pombe_by_inparanoid
Name Last modified Size Description
Parent Directory -
wormpep.08-22-2019.fasta.gz 2023-06-29 09:53 5.1M
orf_trans_all_Candida_glabrata.08-22-2019.fasta.gz 2023-06-29 09:53 2.0M
orf_trans_all_Schizosaccharomyces_pombe.06-26-2014.fasta.gz 2023-06-29 09:53 1.5M
pompep.08-22-2019.fasta.gz 2023-06-29 09:53 1.4M
inparanoid_output.05-23-2012.txt 2023-06-29 09:53 1.2M
inparanoid_output.08-22-2019.txt 2023-06-29 09:53 1.1M
C_glabrata_CBS138_S_pombe_orthologs.txt 2019-08-22 11:25 151K
rejected_sequences.wormpep.08-22-2019.fasta.gz 2023-06-29 09:53 3.1K
This directory contains the orthology assignments between C. glabrata CBS 138 and S. pombe.
The assignments were made using InParanoid version 3.0 (http://inparanoid.sbc.su.se/).
To run InParanoid, the current set of C. glabrata CBS 138 protein sequences from CGD
were compared to the latest set of S. pombe proteins from the Sanger Institute;
the set of C. elegans 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:
C_glabrata_CBS_138_S_pombe_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
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.
orf_trans_all_C_glabrata.MM-DD-YYYY.fasta.gz - the C. glabrata CBS 138 protein file used as input
orf_trans_all_Schizosaccharomyces_pombe.MM-DD-YYYY.fasta.gz - the S. pombe protein file used as input
wormpep.MM-DD-YYYY.fasta.gz - the C. elegans protein set used as an outgroup
inparanoid_output.MM-DD-YYYY.txt - the raw output from InParanoid
rejected_sequences.wormpep.MM-DD-YYYY.fasta.gz - the sequences rejected due to the worm 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.