When comparing genes from two sequenced genomes, how does one determine whether two genes are orthologous? What pitfalls arise when one or both of the genomes are not sequenced?

Sanders 3rd Edition
Ch. 16 - Genomics: Genetics from a Whole-Genome Perspective
Problem B.13Imagine yourself in the same position as Kristen Powers, faced with the decision of whether or not to undergo a genetic test that will discover if you have inherited Huntington disease. List five life decisions or choices that you think are likely to be affected by the results of the genetic test. Do you think you would make the same choice to test that Kristen made? Why or why not?
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Key Concepts
Genetic Testing and Inheritance
Psychological and Ethical Implications of Genetic Information
Impact of Genetic Information on Life Planning
What is a reference genome? How can it be used to survey genetic variation within a species?
The two-hybrid method facilitates the discovery of protein–protein interactions. How does this technique work? Can you think of reasons for obtaining a false-positive result, that is, where the proteins encoded by two clones interact in the two-hybrid system but do not interact in the organism in which they naturally occur? Can you think of reasons you might obtain a false-negative result, in which the two proteins interact in vivo but fail to interact in the two-hybrid system?
Go to http://blast.ncbi.nlm.nih.gov/Blast.cgi and follow the links to nucleotide BLAST. Type in the sequence below; it is broken up into codons to make it easier to copy.
5' ATG TTC GTC AAT CAG CAC CTT TGT GGT TCT CAC CTC GTT GAA GCTTTG TAC CTT GTT TGC GGT GAA CGT GGT TTC TTC TAC ACT CCT AAG ACT TAA 3'
As you will note on the BLAST page, there are several options for tailoring your query to obtain the most relevant information. Some are related to which sequences to search in the database. For example, the search can be limited taxonomically (e.g., restricted to mammals) or by the type of sequences in the database (e.g., cDNA or genomic). For our search, we will use the broadest database, the 'Nucleotide collection (nr/nt).' This is the nonredundant (nr) database of all nucleotide data (nt) in GenBank and can be selected in the 'Database' dialogue box. Other parameters can also be adjusted to make the search more or less sensitive to mismatches or gaps. For our purposes, we will use the default setting, which is automatically presented. Press 'BLAST' to search. What can you say about the DNA sequence?
Select one of the hereditary conditions from either the RUSP core conditions list or the RUSP list of secondary conditions and do some online research to find the following information:
The symptoms and consequences of the condition if it is not treated.
Select one of the hereditary conditions from either the RUSP core conditions list or the RUSP list of secondary conditions and do some online research to find the following information:
The defect that characterizes the condition.