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I have the UNIPROT IDs, PDB IDs and FASTA files of several known proteins. I am looking for a tool that can take as input the protein's amino acid sequence and display the coding nucleotides of those amino acids. Moreover, I look for a tool that would be able to display those nucleotides' location on the human genome.

The final outcome I desire to achieve is to find SNPs in the exons of the protein.

A tool that can handle several amino acid sequences at once is preferred for I have plenty of proteins. I've tried to use UCSC's BLAT human genome search but it was too cumbersome. I've also tried BLAST, but I'd like a more "straightforward" method for displaying the genome locus for each protein. By the way, I've tried to use UCSC's Table Browser but couldn't query several genes simultaneously.

Thank you for your assistance.

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  • $\begingroup$ For something "straightforward" you'd need the correct reading frame, strand orientation, and splicing to get back to a nucleotide sequence to align to the genome. The tools mentioned should help take a lot of work out of this. $\endgroup$
    – Alex Reynolds
    Jan 14, 2018 at 18:39

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I think the mistake here is thinking that you need to use the sequence in order to find the genome co-ordinates. If these proteins come from a well annotated speices, you can easily do this with BioMart.

  1. Go the the ENSEMBL web site.

  2. From the top menu, select BioMart

  3. Under "-CHOSE DATABASE-" select Ensembl Genes, and under "-CHOOSE DATASET-" select your species (eg. Human Genes).

  4. Select "Filters" from the lefthand menu and then expand the "GENE" section.

  5. Select the "Input external references ID list [Max 500 advised]" and from the drop-down select "PDB IDs" or the correct "Uniprot KB" ID.

  6. Paste your IDs into the box.

  7. Select "Attributes" on the left-hand menu. Making sure you've the "Fetaures" radio box select, you can select Chromosome and either Gene Start/Gene End or Transcript start/Transcript end from the GENE section. These coordinates will also contain the untranslated regions unfortunately. You may also want to play about with the various things under "PROTEIN DOMAINS AND FAMILIES", particurlarly under "Protein Features", although I'm not sure what they all mean.

  8. When you are happy with the selection, select the big "Results" at the top to get the coords.

You can also get out Sequences for both the full transcript and the CDS and known germline and somatic variants that fall within the boundaries of the genes.

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  • $\begingroup$ Thank you, very useful tool. Can it display the external results references IDs (ie the PDB IDs) at the results page? $\endgroup$
    – Adrian Smith
    Jan 15, 2018 at 20:14
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Have you tried BLAST, or specifically tBLASTn? This will take a protein and compare it any set of reference genomes. You can also BLAST multiple sequences at once.

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  • $\begingroup$ I've tried it, but I look for a more "straightforward" method for displaying the genome locus for each protein. By the way, I've tried to use UCSC's Table Browser but couldn't query several genes simultaneously. $\endgroup$
    – Adrian Smith
    Jan 13, 2018 at 21:17
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    $\begingroup$ I think that you will have to define "straightforward" if you want help. BLAST and BLAT are the standard tools. You need to describe what issues you have with those tools and what you would like instead. $\endgroup$
    – Bioathlete
    Jan 13, 2018 at 22:47

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