Hi Bryan,
i have seen programs where you say e.g. "fubar" and then the alignment has a part with ">fubar" then everything between ">fubar" and the next ">" is defined as the target sequence (IIUC).
OK, this is easy - simply select the sequence with a keyword (which may be a database record identifier) as target.
... anyways, how is the target sequence used that a consensus sequence couldn't be used instead? i mean, the model looks like it has one applied to it.
Many current algorithms only work with pairwise alignments, and therefore require a target sequence, e.g. delete residues from the model that align with gaps in the target. Some of these concepts can be generalized to multiple sequence alignments, and make these decisions based on the local sequence similarity (calculated from residue substitution scores taking nearby residues into account), but not all (e.g. if a Phe in the model aligns with a Gly in the target, one would possibly want the Phe sidechain to be deleted). One could possibly get away without a target sequence by selecting the right algorithms, but I am wondering whether this has any relevance to current practice. The sequence of the protein is usually known, and indeed used in the homology search to provide template models. BW, Gabor