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BlastX vs TBlastX

BlastX vs TBlastX - Bioinformatics

BlastX vs TBlastX - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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  #1  
Old 10-15-2010, 02:03 PM
Pipette Filler
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Default BlastX vs TBlastX



I need to annotate a huge EST library. I am using Blast2Go to do it, and I am getting different hints when using BlastX vs TBlastX

I would like to hear commentaries about this, what are your thoughs in relation to sensitivity, especificity, etc...

In other words, what will you use for this purpose ?
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Old 11-06-2010, 08:39 PM
Pipette Filler
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Default Re: BlastX vs TBlastX

"Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. 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 and is used extensively in analyzing EST sequences."

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"tblastx takes a nucleotide query sequence, translates it in all six frames, and compares those translations to the database sequences dynamically translated in all six frames. This effectively performs a more sensitive blastp search without doing the manual translation.

tblastx gets around the potential frame-shift and ambiguities that may prevent certain open reading frames from being detected. This is very useful in identifying potential proteins encoded by single pass read ESTs. In addition, it can be a good tool for identifying novel genes.

This type of search is computationally intensive and should be used only as last resort. Searching with large genomic queries is not recommended. For users with regular or batch need for this time of searches, the best way is to install standalone blast and perform the search locally."
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I would initially do a blastx and run tblastx on confirmed hits to get a more ideal result.
tblastx is much more sensitive but it burns a lot of computational time.
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