Biotechnology and Bioinformatics: Bioinformatics Essential Idea: Bioinformatics is the use of computers to analyze sequence data in biological research.

TOK Knowledge claims justified by reference to databases raise unique knowledge questions. How reliable are knowledge claims justified by reference to data sources developed for different purposes by different researchers using different methods?

Databases A database is a set of related data that has been organized and made available for access by many users. This data can be easily accessed by users anywhere in the world.

Due to the rapid increase in data acquisition and the ease of input of this data into such databases, the amount of information being stored is increasing exponentially--essentially doubling every 18 months. Databases

Databases In the biological sciences, DNA sequence and protein sequence data is the most often accessed. These databases can be searched to compare newly identified sequences with sequences of known function in other organisms.

This allows researchers to use multiple sequence alignment to look at the evolutionary relationship of the organisms being studied--such as with phylogenetics. Databases

Multiple Sequence Alignment When studying evolutionary relationships, scientists often look at the sequences of multiple organisms.

Multiple Sequence Alignment The gene function and the gene sequence can be studied in model organisms with similar sequences to learn more about them. This allows researchers to make inferences, develop hypotheses, and to design and test treatment protocols for people with genetic disorders.

Sequence Alignment Sequence alignment software is what allows people to make a comparison of sequences from different organisms. This software can be accessed online. For instance, the SDSC Biology Workbench we’ve used. Searching databases for comparative purposes allows newly identified sequences to be compared with sequences of known function in other organisms.

BLAST BLAST stands for Basic Local Alignment Search Tool. It is an algorithm for comparing biological sequence information. Users input and access data from anywhere. There are many different ways in which this can be used. BLASTn is a nucleotide sequence alignment tool. BLASTp is a protein alignment tool.

BLASTn Using this program, a DNA sequence can be input and the software will return the most similar DNA sequences from the DNA database specified by the user.

BLASTp As with the BLASTn, BLASTp allows the user to query a protein sequence and get the most similar protein sequence from the specified database.

EST EST stands for Expressed Sequence Tag. Living organisms produce mRNAs from splicing together exons.

In vitro studies of tissue samples of organisms about which little is known allows for the reverse transcription of these mRNA transcripts to yield cDNA that corresponds to the genes expressed in that tissue. EST

Thus, an EST is a short “sub-sequence” of cDNA. It is often used to identify gene transcripts, and plays an important role in gene discovery and sequence determination. Simply put, the cDNA is complementary to mRNA and represents portions of expressed genes. This technique allows for a comparison ESTs from lesser-known species with those from a species whose genome has been well-characterized enabling researchers to identify the function of gene loci in the new organism. EST

The development of a complete EST library is an important step in the mapping of a new genome. ESTs can be mapped to specific chromosome locations using a variety of methods (radiation hybrid mapping, Happy mapping, FISH). EST

EST Uses ESTs give information that allows for the design of DNA microarrays and subsequent determination of gene expression.

EST Uses The use of EST information gives researchers knowledge about the function of a gene. This information can be used in the diagnosis and treatment of disease. Researchers are currently designing methods to mine databases for EST information and gene discovery.

Gene Knockout Technology Gene knockout technology is also used to determine the function of a gene. This technique is commonly used on mice and other model organisms. In this process, a gene that has been sequenced, but for which little to no function is known is “knocked out” of the organism.

Gene Knockout Technology Organisms in which the gene has been knocked out are compared to normal organisms enabling researchers to draw conclusions about the function of the gene.

How it Works: The genetic information of individual cells is altered in some way creating a transgenic animal with an altered gene. Once this has been accomplished, the goal is to get embryonic stem cells transformed and inserted into early embryos. This results in animals with a genetic change in their germ-line cells that can pass the genetic alteration on to their offspring.

How it Works: