Molecular Microbial Finger Printing
Schematic of 16s gene amplification of environmental samples.(courtesy of Bruce Fouke's lab)
Microbial Identification: Overview
Collect an environmental sample (learn more) - Collecting samples involves the isolation and careful gathering of specimens of interest in a given environmental study. Methodologies employed can be as involved and diverse as the studies themselves.
Images of students from the Fouke lab sampling at Mammoth Hot Springs, Yellowstone National Park (courtesy of Bruce Fouke's lab).
(learn more) - Extraction of the genetic material from the organisms of interest is the first step in identifying them at the molecular level.
(learn more) - "Sometimes called molecular photocopying, the polymerase chain reaction (PCR) is a fast and inexpensive technique used to "amplify" - copy - small segments of DNA. Because significant amounts of a sample of DNA are necessary for molecular and genetic analyses, studies of isolated pieces of DNA are nearly impossible without PCR amplification" (from the National Human Genome Research Institute ).
Process and analyze the sequences -
Mega BLAST uses a greedy algorithm  for the nucleotide sequence alignment search. This program is optimized for aligning sequences that differ slightly as a result of sequencing or other similar "errors". When larger word size is used (see explanation below), it is up to 10 times faster than more common sequence similarity programs. Mega BLAST is also able to efficiently handle much longer DNA sequences than the BLASTN program of traditional BLAST algorithm.