Biological Databases and Retrieval Systems

In recent years, biological databases have greatly developed, and became a part of the biologist's everyday toolbox (see eg. [4]). There are several reasons to search databases, for instance:

1.

When obtaining a new DNA sequence, one needs to know whether it has already been deposited in the databanks fully or partially, or whether they contain any homologous sequences (sequences which are descended from a common ancestor).

2.

Some of the databases contain annotation which has already been added to a specific sequence. Finding annotation for the searched sequence or its homologous sequences can enhance the progress of the research .

3.

To find similar non-coding DNA stretches in the database: for instance Repeat elements or regulatory sequences.

4.

There are other uses for specific purpose, like locating false priming sites for a set of PCR oligonucleotides.

5.

Given a putative coding ORF, we can search for homologous proteins - proteins similar in their sequence and therefore also intheir presumed folding or structure or function.