BLAST (Basic Local Alignment Search Tool)
Introduction
BLAST was developed by Altschul. et al, and it was published on Journal of Molecular Biology(J. Mol. Biol. 215:403-410(1990)).
BLAST(Basic Local Alignment Search Tool) is analysis tools/suits of similarity between sequences with nucleotide or protein databases.
BLAST programs makes sequences compare with open-access databases for similarities.
The results from BLAST operations is relatively statistical data.
BLAST proceeds local algorithms to demonstrate the similarities of two sequences, for example, two sequences alignment.
Capabilities and Usage
BLAST makes several sequences input compare with each data stored in many nucleotide or protein databases.
BLAST proceeds compares of homologous similarities between sequences input and data stored in databases.
While operating BLAST, the searching database must be a single type, for instance, proteins.
There are flexible operations, nucleotide sequence input compares with protein databases or protein sequence input compares with protein databases.
The suits prepared by GCG and EMBOSS include five kinds of BLAST operations as following:
| Type | Input | Search | Descriptions |
|---|---|---|---|
| BlastP | protein | protein | - |
| BlastX | nucleotide | protein | Nucleotide sequences are (transcribed and) translated into proteins (x6), proteins compare with databases. |
| BlastN | nucleotide | nucleotide | - |
| BlastTN | protein | nucleotide | Nucleotide sequences are (transcribed and) translated into proteins (x6), proteins compare with one input. |
| BlastTX | nucleotide | nucleotide | Both nucleotide sequence input and nucleotide sequence in adtabases are (transcribed and) translated into proteins (x6 / each), and then crossly compare to generate 36 results (gap not considerated). |
Based on the sequence input, choose the better one kind of all BLAST operations. For example, while a compare with both nucleotide-type sequences there are BLASTN or TBLASTX operations you could choose. Usually the default setting is BLASTN, it is for sure to operate two sequences under TBLASTN(gap not considered).
BLAST is also operated on the local/terminal. It is necessary to download public databases and to maintain/update databases.
There are websites providing BLAST operations for free, but if the sequence is quite important, it would be better operating one on the local/terminal.
Algorithms designed
- Unlikely the traditional process in the beginning of the local alignment BLAST first identifies word matches between the query sequence and database sequences in order to speed up the performance of searching. Such matches are then extended in both directions using the concept of the dynamic programming algorithm in one character compare. Such methods may decrease the sensitivity. BLAST has a clever way of maintaining sensitivity. That is, it considers not only identical words, but also " near-identical " words during the word matching.
Explanations
- There are two kinds of evolution relationships are detected in BLAST searches.
- orthology : A speciation event. Orthologous proteins are proteins that carry out the same function but in different species. For example, the human protein ABL is orthologous to the mouse protein ABL.
- paralogy : A gene duplication event. Paralogous proteins perform different but related function in the same organism. For example, ABL1 and ABL2 are paralogous proteins.
References
- Genomics and Bioinformatics。Tore Samuelsson。Cambridge university press。July 2012。ISBN: 9781107401242。