Bioinformatics in India
sequencing
Database searching
Database searching is the application of knowledge gained from previous examination of well-characterised sequences to the problem of discovering the biochemistry and physiology of a newly discovered gene or its protein product.
The objective of a database search is to distinguish sequences related to the query sequence by some model (e.g, evolution) from unrelated sequences. This objective is different from the objective of aligning sequences, which is to discover the most likely history of changes between sequences already inferred to be related. This difference in objectives implies a very different set of choices for parameters and strategies.
A database search is a computational invetigation and like a laboratory investigation, must
be performed thoughtfully A database search perfromed with injudicious parameters will lead
to wrong answers and missed discoveries. While the default parameters on most database search
servers are appropriate to a wide range of the most common circumstances,no single set of
parameters will be the best for all searches.
there are at least three distinct situations where other parameters are likely to give better results
When:
- The sequences in the database that are homologous to the query sequnence are evolutionarily highly diverged.
- Either the query sequence or its homologues in the database are too short to achieve a statistically significant match using the default parameter
- The researcher is interested in finding homologues in only a limited range of species in which the query sequence was found is different from that implied by the default parameters
Database searching helps to evoluate whether a newly determined sequence is related to a previouly determined and characterised gene or protein through a common eevolutionary ancester. Homlogy, relatedness through a common evolutionary ancestor, is not directly observable.In sequence database searching we observe sequence likeness or similarity. If the likeness is great enough,we may infer that the two sequences are homologus thus, much of the previously determined knowledge we apply in database searching involves how to best measure sequence likeness and how to assess whether the observed degree of sequence likeness is sufficient to allow us to infer that the sequences are homologus; that is, related through divergent evolution.
Entrez
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