Basic Applied Bioinformatics

CHAPTER 14BLASTx

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

14.1 INTRODUCTION

BLASTx is one of the three translated BLAST algorithms – namely, BLASTx, tBLASTn and tBLASTx. In BLASTx, a nucleotide sequence is used as a query, which is first translated in all six reading frames, and then each of the translated amino acid sequences is compared to the protein sequences in protein databases. Thus, the comparison occurs at the level of amino acid and, so, the result is the aligned amino acid sequences (i.e., the translated query versus homologous sequence in protein database), although the query is a nucleotide sequence. BLASTx runs at a slower pace, due to matching all the six reading frames to the protein databases. The result ultimately gives the open reading frame as a match with its homologous sequence.

BLASTx is a powerful gene‐finding or gene‐predicting tool. It is recommended for identifying the protein‐coding genes in genomic DNA/cDNA. It is also used to detect whether a novel nucleotide sequence is a protein‐coding gene or not, and it can be used to identify proteins encoded by transcripts or transcript variants.

14.2 OBJECTIVE

To determine the open reading frame and the name of the gene from the given coding sequence (cds).

14.3 PROCEDURE

The basic steps are same as for BLASTn. However, parameters like “Genetic Code”, “Organism”, and “Database” may be required to be modified. Open the NCBI home page with the URL http://www.ncbi.nlm.nih.gov/ ...