Bioinformatics Bioinformatics Tool Sequence Alignment

tBLASTx

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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.

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 day 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. 

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 un-annotated 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:

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

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 tBLASTx is used.

The necessary steps for tBLASTx are the same as for BLASTx. We have to just open the NCBI home page by typing its URL and click “tBLASTx”; alternatively, it can also be opened by entering its URL in the address bar.

Enter query sequences

We have to either enter accession number(s) or pasted FASTA sequence(s). We can paste one or more nucleotide query sequence(s) in FASTA format or upload the sequences containing the file.

tBLASTx is part of the new blast+ package from the NCBI. tBLASTx compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Help on the options available can be found by typing tBLASTx -help. 

Uses 

  • Cross-species gene prediction at the genome or transcript level
  • searching for genes missed by traditional methods or not yet in protein databases
  • Finding protein-coding genes in genomic DNA
  • determining if a cDNA corresponds to a known protein

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