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Old 01-13-2011, 05:56 PM   #1
rdu
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Default query required by BLASTX

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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Old 01-14-2011, 05:00 AM   #2
kmcarr
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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).
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Old 01-14-2011, 09:45 AM   #3
rdu
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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.
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Old 01-14-2011, 10:41 AM   #4
Mgollery
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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.
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Old 01-14-2011, 11:13 AM   #5
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Thanks. Let me take a try.
Have a good day to everyone!
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