I'm trying to align an 800-amino-acid sequence coded by a gene from a
known genome to a large set of ordered contig sequences from a new
genome of a related strain whose sequence is not yet fully resolved.
Using tblastn, I've so far been unsuccessful in finding
positions/sequence sections that align well to the sequence
from the gene of interest and also do not align better to another
sequence from another gene.
Effectively, sequences that have the best alignment to a gene get
'taken' by that gene, leaving the gene of interest with no significant
alignments. Thus, I’m unable to map the position/sequence sections of
this gene among the contigs.
Is there a way I can decisively check whether or not this gene exists
in its entirety, or partially, in the contig set
of the newly sequenced genome, and if yes, determine its location?
Or is there something inherently flawed about my method/approach that
I could please get a recommendation as to how to correct?