Blastall Batch Utility: Introduxtion

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 Blastall?
  The NCBI Blast program is freely downloadable from NCBI web site (ftp://ftp.ncbi.nih.gov/blast) for running it locally. One of its modules is Blastall, which supports all the five Blast programs (blastp, blastn, blastx, tblastn and tblastx). Instead of running Blast online, a user can use Blastall on his own computer, with the advantage of more flexibility and higher performance. A related program, formatdb, also included in the downloaded package, is used to format Fatsa files for use as Blast databases.

• What is the Blastall Batch Utility?
  The Blastall Batch Utility is an online web application used for generating command strings and batch files for running the Blastall program locally. The interactive user interface lets the user select input files, define running parameters and creates a corresponding batch file on the user's local hard disk.

• What are the Blast/Blastall programs?
  There are five programs:
  • blastn
    compares a nucleotide query sequence against a nucleotide sequence database.
  • blastp
    compares a protein query sequence against a protein sequence database.
  • blastx
    compares a nucleotide query sequence translated in all reading frames against a protein sequence database. You could use this option to find potential translation products of an unknown nucleotide sequence.
  • tblastn
    compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames.
  • tblastx
    compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Note: gapped alignments are not available with tblastx.

• What are the batch utility modules?
  There are three modules, each creates a batch file to be run locally:
  • 1. To Blast a Fasta File vs. another Fasta File
  • 2. To Blast a Fasta File vs. a Blast database
  • 3. To Format a Fasta File as a Blast Database

• What are the Simple (fast) and Advanced versions?
  Each of the Blast modules can be run in either of the following versions:
  • 1. Simple (fast) version: This version functions mainly on the client, and its responsiveness is fast. However, it does not support setting of Blast parameters.
  • 2. Advanced version: This version functions mainly on the server, and any selection or data entry involves sending the data over the net. Therefore its responsiveness is slower, requiring to wait for the window to be updated. This version does support setting and modifying Blast run parameters.

• How to use the Blastall Batch Utility?
  Detailed helps is available on the separate pages of this utility. Click on one of the buttons on this page to select the required task. You will be moved to the corresponding page, where the Instructions button can be clicked to display a help file.