Bioinformatics Sequence Alignment

BLAST Variants

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The Basic Local Alignment Search Tool (BLAST) finds regions of similarity between sequences. The program compares nucleotide or protein sequences and calculates the statistical significance of matches. BLAST can be used to find out the functional and evolutionary relationships between sequences as well as help identify members of gene families.

The five traditional BLAST programs are BLASTn, BLASTp, BLASTx, tBLASTn, and tBLASTx. BLASTn compares nucleotide sequences to one another (hence the n). All other programs compare protein sequences.

BLASTn compares a DNA query to a DNA database. It searches both strands automatically. It is optimized for speed, rather than sensitivity.


  • Mapping oligonucleotides
  • cDNAs
  • PCR products to a genome
  • Screening repetitive elements
  • Cross-species sequence exploration
  • Annotating genomic DNA
  • Clustering sequencing reads
  • Vector clipping

BLASTp compares a protein query to a protein database.


  • Identifying common regions between proteins
  • collecting related proteins for phylogenetic analyses

BLASTx compares a DNA query to a protein database, by translating the query sequence in the 6 possible frames, and comparing each against the database (3 reading frames from each strand of the DNA) searching.


  • Finding protein-coding genes in genomic DNA
  • determining if a cDNA corresponds to a known protein

tBLASTn compares a protein query to a DNA database, in the 6 possible frames of the database.


  • Identifying transcripts, potentially from multiple organisms, similar to a given protein
  • mapping a protein to genomic DNA

tBLASTx compares the protein encoded in a DNA query to the protein encoded in a DNA database, in the 6*6 possible frames of both query and database sequences.


  • Cross-species gene prediction at the genome or transcript level
  • searching for genes missed by traditional methods or not yet in protein databases

BLAST2 is an advanced BLAST. It can perform gapped alignments.

PSI-BLAST is a Position Specific Iterated BLAST that performs iterative database searches.

We can also find many BLAST derivatives and BLAST wrappers (scripts that run BLAST in a specialized way) with names such as PSI-BLAST, PHI-BLAST, MegaBLAST, BLASTZ, XBLAST, MPBLAST, HT-BLAST, and GENE-BLAST. 

Nowadays, large quantities of gene sequences of related species of plants, animals and microorganisms show complex patterns of similarity to one another and many molecular biologists are convinced that an understanding of sequence evolution is the first step towards understanding the evolution itself. There are varieties of different tools available to perform sequence analysis. Blast is a successful tool to compare biological sequences. Now a days Large amount of biological data is available, So Standalone Blast is not sufficient to handle all types of queries related to sequence similarities, so different variants such as BlastX, BlastP, BlastN, TblastN, TblastX, PSI_Blasts, have been developed. Each variant has limitations and advantages. Every tool is made to handle different purposes. 

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