Putative horizontally transfered genes

[Alejandro]

Hello, I am analyzing putative horizontally transfered genes between some bacteria and viruses. However, I need to know what the algorithm for this function is. Anybody can help me with this? I need the algorith for a presentation

[Ernest Szeto]

From the source code comments ...

#!/usr/bin/env perl
# Identify horizontal transfer genes.
#
# Algorithm:
#
#   1. Find block of top hits within 0.95 of the maximum bit score.
#   2. For each hit in this block, find the highest phyla that is
#      different from the query gene's genome.  E.g., if domain is
#      different, record the external domain of the transfer. Next,
#      if the domain is same, but phylum is different, record the
#      the phylum. And so forth downwards to the 'order' level.
#   3. We do not include cases where the query gene's genome phyla is
#      the only one in the database, since "everything is external"
#      due to this artifact of the database, and is not the biology.
#   4. Also report the reverse hit from the subject taxon/gene
#      to the same phyla as query genome for the query gene with
#      the horizontal transfer.  This is a phyla reverse hit with
#      no bit score restrictions. 
#