DNA translate tool with nucleotide/AA numbers

[Valeria Vvasta@UW.Edu]

Hello,

I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number such as this

I'd appreciate any suggestion

thanks

Valeria

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

You can use BLAT to view an alignment of a protein sequence, and it will provide you with a visual that contains the nucleotide and protein number. For example, if you go to the BLAT tool for the hg38 assembly and search for the following protein sequence:

https://genome.ucsc.edu/cgi-bin/hgBlat?db=hg38

MPRSCCSRSGALLLALLLQASMEVRGWCLESSQCQDLTTESNLLECIRACKPDLSAETPM
FPGNGDEQPLTENPRKYVMGHFRWDRFGRRNSSSSGSSGAGQKREDVSAGEDCGPLPEGG
PEPRSDGAKPGPREGKRSYSMEHFRWGKPVGKKRRPVKVYPNGAEDESAEAFPLEFKREL
TGQRLREGDGPDGPADDGAGAQADLEHSLLVAAEKKDEGPYRMEHFRWGSPPKDKRYGGF
MTSEKSQTPLVTLFKNAIIKNAYKKGE

After performing the search, you will see a "details" link that will give you a side-by-side alignment like your shared image. BLAT will also allow you to change "Query type:" to "translated DNA" to perform a similar search using a nucleotide sequence.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro

UCSC Genome Browser

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