Suppose your sequences are stored in seq1.fna, seq2.fna. 
Type the command line: 
java -jar PH.jar -i seq1.fna -j seq2.fna
to compare the two sequences. If you are running the 
PatternHunter demo version, replace "java -jar PH.jar" 
with "ph". 

Current software is too slow, runs out of memory and is 
unreliable in many applications that compare large amounts 
of data. 

PatternHunter is a general purpose homology search 
software. It is many times faster than Blast and is more 
sensitive. 

Pharmacogenetics is a subset of pharmacogenomics which uses 
genomic/bioinformatic methods to identify genomic 
correlates, for example SNPs (Single Nucleotide 
Polymorphisms), characteristic of particular patient 
response profiles and use those markers to inform the 
administration and development of therapies. Strikingly, 
such approaches have been used to "resurrect" drugs thought 
previously to be ineffective, but subsequently found to 
work with in subset of patients. They can also be used for 
optimizing the doses of chemotherapy for particular 
patients.

proteomics is "qualitative and quantitative studies of gene 
expression at the level of the functional proteins 
themselves" that is "an interface between protein 
biochemistry and molecular biology".

Mathematical biology or biomathematics is an
interdisciplinary field of academic study which aims at
modeling natural, biological processes using mathematical
techniques and tools. It has both practical and theoretical
applications in biological research.

The combination of chemical synthesis, biological 
screening, and data-mining approaches used to guide drug 
discovery and development" 

is the use of computer and informational techniques, 
applied to a range of problems in the field of chemistry. 
These in silico techniques are used in pharmaceutical 
companies in the process of drug discovery. These methods 
can also be used in chemical and allied industries in 
various other forms.

Early symptoms of the disease can often be difficult to 
detect but may include dieback of the limbs and branches, 
yellowing of foliage, splits in the trunk of the infected 
tree, poor vigour, exudates from the trunk (kino 
production), scars may form on the trunk and darkening of 
the larger roots.

Removal of the bark may reveal the presence of mycelial 
fans ? these are large sheets of fungal growth, usually 
white in colour, which will have a characteristic mushroom 
odour. The surface of the affected timber is often pitted 
in appearance. 

The fungus produces mushrooms in May?June. These are olive 
brown to yellow in colour, can be up to 12 cm in diameter 
with a stipe (stalk) of up to 15 cm high, although usually 
less. The stipe will have an annulus (the ring of tissue 
around the stipe) that should be quite obvious. The spores 
of the fungus are white and these often coat the surface of 
the mushrooms.

At flowering a cloudy, tan, sticky "honeydew" may appear on 
the florets, especially if the weather is humid. The most 
noticeable signs of the disease, though, are the sclerotia 
which protrude from the glumes and are produced as the host 
plant matures. The sclerotia that contaminate harvested 
grain are easily seen because they are dark.

The distinctive underground symptoms of club root have 
earned it the nickname "fingers and toes". These symptoms 
consist of swellings on the roots and occasionally on below 
ground stems. Swellings range from small round enlarged 
areas to large spindle-shaped galls. All or part of the 
root system may be affected. In cases of mild infection no 
above ground symptoms may be evident. In severe cases, 
nutrient absorption and water uptake are disrupted and 
above ground symptoms are those commonly associated with 
nutrient deficiencies and drought stress. Plants may show 
varying degrees of yellowing (chlorosis). Infected plants 
may also wilt during the hot part of the day. Flagging, 
wilting of uppermost leaves is common on young infected 
plants. Premature death, stunting and reduced size and 
quality of heads are also symptoms associated with club 
root.

Epidemiologists use specific terminology to accurately 
communicate magnitudes and potentials for disease 
Incidence: the number or proportion of plant units diseased 
Severity; the proportion of area or amount of plant tissue 
that is diseased 
Yield loss; the proportion of yield that a grower will not 
be able to harvest due directly to the disease 
Economic loss; the reduction in economic returns due to 
disease. What about compensation of plants which results in 
no yield loss though one has up to 50% plants lost due to 
disease? Think about the "Green Revolution". 
Economic threshold; when the amount of gain from control 
equals the amount of estimated loss from the disease

On leaves, young infections are very small, greenish-
yellow, translucent spots that are difficult to see. With 
time the lesions enlarge, appearing on the upper leaf 
surface as irregular pale-yellow to greenish-yellow spots 
up to 1/4 inch or more in diameter. On the underside of the 
leaf, the fungus mycelium (the "downy mildew") can be seen 
within the border of the lesion as a delicate, dense, white 
to grayish, cotton-like growth. Infected tissue gradually 
becomes dark brown, irregular, and brittle. Severely 
infected leaves eventually turn brown, wither, curl, and 
drop. The disease attacks older leaves in late summer and 
autumn, producing a mosaic of small, angular, yellow to red-
brown spots on the upper surface. Lesions commonly form 
along veins, and the fungus sporulates in these areas on 
the lower leaf surface during periods of wet weather and 
high humidity.