I am using InParanoid software for identify orthologs genes between strains of one specie. So, I expect to find very similar genes shared into both genomes.
In a typical reciprocal blast, I set the cut off with and E-Value of 1e-7 and a %identity (pident) of 85%. However, InParanoid has more parameters to fit the similarity.
If I need an e-value of 1e-7 and a %identity of 85%, what are the values for the configuration variables of InParanoid?
The default settings are:
score_cutoff = 40; # In bits. Any match below this is ignored #
outgroup_cutoff = 50; # In bits. Outgroup sequence hit must be this many bits stronger to reject best-best hit between A and B
conf_cutoff = 0.05; # Include in-paralogs with this confidence or better #
group_overlap_cutoff = 0.5; # Merge groups if ortholog in one group has more than this confidence in other group
my $seq_overlap_cutoff = 0.5; # Match area should cover at least this much of longer sequence. Match area is defined as area from start of first segment to end of last segment, i.e segments 1-10 and 90-100 gives a match length of 100.
my $segment_coverage_cutoff = 0.25; # Actually matching segments must cover this much of longer sequence.
I put the $score_cutoff = 85 instead 40, but when I obtain the pair genes, the list shows scores since 4500 to 85. I don't undestand this...
OrtoID Score OrtoA OrtoB
1 4580 genA 1.000 genB 1.000
...... (more rows...)
4359 85 genX 1.000 genY 1.000
I will appreciate any help!!!
Thankd in advance.