Bioinformatics Tools: Interactive Blast Query

Overview / Faq

• What is Bioinformatics
  The merger of biotechnology and information technology with the goal of revealing new insights and principles in biology. Bioinformatics is the application of computer technology to the management of biological information.

• Is Bioinformatics related to Artificial Life?
  Not really, but some relation exists. Both live in the area integrating biology and computers. In bioinformatics computer science is used to find specific insights in biology. In artificial life computers are used to find more general and conceptual insights about biology. In some fields of artificial life, the reverse is done: Mechanisms found in biology are used to solve some problems of computer science (e.g. genetic algorithms).

• What is Blast
  Blast: Basic Local Alignment Search Tool. A sequence comparison algorithm, optimized for speed, used to search sequence databases for optimal local alignments to a query. Sequence alignments provide a powerful way to compare novel sequences with previously characterized genes. Both functional and evolutionary information can be inferred from well designed queries and alignments. BLAST provides a method for rapid searching of nucleotide and protein databases. Since the BLAST algorithm detects local as well as global alignments, regions of similarity embedded in otherwise unrelated proteins can be detected. Both types of similarity may provide important clues to the function of uncharacterized proteins.

• What is the Interactive Blast Query?
  The Interactive Blast Query uses Ncbi Blast server, and queries the Ncbi Blast database. It adds two output formats to those offered by the Ncbi Blast program, and both of them are interactive, allowing online manipulation of the data. The two interactive formats are:
  • Filter/Sort Hit Table - allowing extensive filtering and sorting of the data, meaning that the user can choose to view only a subset of the full output, according to specified criteria, sorted to the users specifications. The data is displayed in small chunks, and moving between the pages (paging) is supported.
  • Master/Detail Hit Table - Allowing to view the alignments of each hit in an interactive and user-friendly master/detail table. Here, too, sorting and paging are supported.

• How it works?
  The data is brought to the user machine from the Ncbi server, and once it is retrieved it can be handled as is if it were stored in a local databse. It can be continuously played with as long as the user has not quitted the application. The data can be filtered, sorted, rearranged and moved back and forth between the two hit table formats.

• In what language is it written?
  The program is written in C#, using the Asp.Net technology of Microsoft's .Net framework.

• What about detailed instructions?
  Each page includes a help button which displays a specific instructions page.