Basic Applied Bioinformatics

CHAPTER 16tBLASTx

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

16.1 INTRODUCTION

tBLASTx, or translated BLASTx, accepts nucleotide query sequence(s) as well as database subject sequences, translates both to 6‐frame amino acid sequences and, finally, compares them at the amino acid level. tBLASTx is a valuable tool for discovering novel genes in the nucleotide sequences, such as single pass expressed sequence tags and draft genome records which are unannotated and riddled with errors (e.g., wrong bases and frame shifts). These errors often make one coding sequence difficult to be detected. However, the limitations associated with tBLASTx are:

1. tBLASTx is very much resource‐intensive and time‐consuming;
2. large queries are not recommended, due to the inherent limitation of the time required.

16.2 OBJECTIVE

To determine the homology of a given nucleotide query sequence against the database of draft genome records, as well as expressed sequence tag data to identify the sequence.

16.3 PROCEDURE

The necessary steps are the same as for BLASTx. Open the NCBI home page by typing http://www.ncbi.nlm.nih.gov/and click “tBLASTx”; alternatively, it can also be opened by entering the URL in the address bar: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome.

16.3.1 Enter query sequences

• Enter accession number(s) or FASTA sequence(s): Paste one or more nucleotide query sequence(s) in FASTA format, or ...