Bioinformatics Bioinformatics Tool Sequence Alignment


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It 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.

Blastx is used when we want to compare a nucleotide sequence to a protein DB but as we cannot compare nucleotides and protein to each other directly the nucleotide sequence is translated (in all 6 frames, this is important) and then an amino-acid vs amino acid comparison is done.

There are three varieties of translated BLAST search; “tBLASTn,” “BLASTx,” and “tBLASTx.” In the first variant, “tBLASTn,” a protein sequence query is compared to the six-frame translations of the sequences in a nucleotide database. In the second variant, “BLASTx,” a nucleotide sequence query is translated in six reading frames, and the resulting six-protein sequences are compared, in turn, to those in a protein sequence database. In the third variant, “tBLASTx,” both the “query” and database “subject” nucleotide sequences are translated in six reading frames, after which 36 (6 × 6) protein “BLASTp” comparisons are made. Protein sequences are better conserved than their corresponding nucleotide sequences. Because the translated searches make their comparisons at the level of protein sequences, they are more sensitive than direct nucleotide sequence searches. A common use of the “tBLASTn” and “BLASTx” programs is to help annotate coding regions on a nucleotide sequence; they are also useful in detecting frame-shifts in these coding regions. The “tBLASTx” program provides a sensitive way to compare transcripts to genomic sequences without the knowledge of any protein translation; however, it is very computationally intensive. MegaBLAST can often achieve sufficient sensitivity at a much greater speed in searches between the sequences of closely related species and is preferred for batch analysis of short transcript sequences such as expressed sequence tags.

BLASTx compares a nucleotide query sequence that is translated in six reading frames (resulting in six protein sequences) against a database of protein sequences. Because BLASTx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus BLASTx is often the first analysis performed with a newly determined nucleotide sequence.

We just have to paste the query sequence in nucleotide form and run the BLASTx search to obtain a result similar. The translation of the query sequence in 6 reading frames is shown in results to find similarity to the rest of the protein sequence. 


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

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