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From the website, "BLASTX search protein databases using a translated nucleotide query." What does "a translated nucleotide query" really mean here? Shouldn't be a initial genomic DNA sequence, right? A mRNA sequence with "U" replaced by "T"? Would appreciate any help or hint!
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The input (query) which you provide to BLASTX is standard DNA sequence (AGCTN). The BLASTX program then translates this input into protein sequence; the translation is performed for all six possible reading frames. This is what is meant by "translated nucleotide query". The translated sequences are then compared to the protein database you have specified. I don't know off the top of my head how BLASTX deals RNA sequences (AGCUN). -
Thanks.
Yes, I understand the input should be a standard DNA sequence. The thing confusing me is this DNA sequence should only compose of protein coding parts, or it just a common DNA sequence. That's why I mentioned mRNA sequence with "U" replaced by "T".
Actually, I got a initial genomic DNA sequence data, I try to BLAST it vs. a protein database to have functional analysis, just wondering if i need more steps, or can straightly take BLASTX running.Comment
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Hello
No, you don't need any more steps, you can just submit as is to the protein database. Although, if this is a non-coding region, you won't find much.Comment
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Thanks. Let me take a try.
Have a good day to everyone!Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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