Here you can find the | ORF-finder | input-DNA |  Annotation  |  DNA_pattern_find |  home |


Paste the sequence into the window in FASTA format:
(see example protein sequence for the correct format)

Show   results
Background information

BLAST is an acronym for Basic Local Alignment Search Tool.

BLAST is the most frequently used bioinformatics program.

A BLAST search allows you to make a comparison between an unknown input sequence (also called QUERY) with a database that contains DNA and protein sequence information. The program identifies those sequences that have the best homology with the query sequence (so-called HITS). The extent of homology is expressed as the BIT-score. The maximum score found with a perfect match depends on the length of the query sequence and in case of a protein sequence, the type of the amino acids. On average, a match between two identical amino acids gives a score of 2 bits. So a query sequence of 150 amino acids gives a maximum score of 300 BITs.


BLAST can search in a protein database in two ways:
  1. In the BLASTP mode the input sequence consists of amino acids that is compared with a library of protein or amino acid sequences.
  2. In the BLASTX mode the input sequence consists of DNA. This DNA sequence is first automatically translated into all possible amino acid sequences that are compared with all translated DNA sequences. In the BLASTX mode an input sequence of 450 nucleotides has a maximal BIT score of 300. Can you explain this?

The BLAST version used here only uses the BLASTP mode. Translation of the DNA into open reading frames we do with the ORF-finder.
Other versions of this program have modes such as BLASTN; using a DNA query with a DNA database.