programming-for-dummies

Searching Databases 629
✦ Swiss-Prot stores protein sequences.
✦ OMIM (Online Mendelian Inheritance in Man) stores human genes and
genetic disorders data.
After you find a particular sequence, you can look up articles about particular
sequences in PubMed, a database of articles published in biomedical and
life science journals.
Although it’s possible to search these databases manually, it’s usually much
faster and easier to write a program that can send a list of sequences to a
database, search that database for known sequences that match the ones
sent, and then retrieve a list of those known sequences for further study.
Because searching databases is such a common task, biologists have created
a variety of tools to standardize and simplify this procedure. One of the more
popular tools is Basic Local Alignment and Search Tool, otherwise known as
BLAST.
BLAST can look for exact matches or just sequences that are similar to yours
within specified limits, such as a sequence that’s no more than ten percent
different. This process of matching up sequences is sequence alignment or
just alignment.
By finding an exact match of your sequence in a database, you can identify
what you have. By comparing your sequence with similar ones, you can
better understand the possible characteristics of your sequence. For example,
a cat is more similar to a dog than a rattlesnake, so a cat would likely
behave more like a dog than a rattlesnake.
The BLAST algorithm and computer program was written by the U.S. National
Center for Biotechnology Information (NCBI) at Pennsylvania State
University (www.ncbi.nlm.nih.gov/BLAST).
Book VII
Chapter 2
Bioinformatics
The basic idea behind BLAST is to compare one sequence (called a query
sequence) with a database to find exact matches of a certain number of
characters, such as four. For example, suppose you had a sequence like this:
ATCACCACCTCCG
With BLAST, you could specify that you only want to find matches of four
characters or more, such as:
ATCACCTGGTATC