how to find in database the genomic sequence corresponding to the amino acid one of a protein

Question

[silvia.caprari84]

Hi all,

do you know how to find in (some) database the genomic sequence of a certain protein starting from the corresponding amino acid sequence?I have an amino acid sequence of a protein and I have to retrieve the corresponding DNA sequence but, looking at the protein in UniProt and NCBI, I was not able to find a link going to the genomic one..There are different identification codes but It seems to me that they link to other information..

Thank you very much ion advance.

Cheers,
Silvia

[5heikki]

Retrieve The Fasta Nucleic Sequences Of A List Of Ncbi Accession Number Of Proteins

Answer 1

[venu]

1. http://www.ncbi.nlm.nih.gov/guide/howto/find-transcript-gene/
2. http://www.ebi.ac.uk/training/online/course/ensembl-browsing-chordate-genomes/guided-examples-using-ensembl/using-sequence-find-gene-blas

There is something special about second one. Convert your protein sequence to nt sequence and follow the instructions, at last you will end up with a gene that codes for your protein and location of base pairs (start to end) that codes for protein.

[silvia.caprari84]

Ok, thank you very much. It is very helpful. Can I also ask if you know how to visualize the DNA regions near to the gene of interest on the genome?

Thank you very much in advance.

Cheers,
Silvia

[venu]

That is also clearly explained in the provided link. It is in step 3, if I remember correctly.

Answer 2

[Antonio R. Franco]

You can do it by using NCBI tBlastN

tBlastN will convert your amino acid sequence to the corresponding nucleic acid, and then, this will be compared to the desired nucleic database. You can even select several different databases to compare.

Answer 3

[Antonio R. Franco]

It depends upon your genome. You have several choices

• if you are working with a model organism, you can use the mapping facilities you can find in MapViewer where you can have the chance to look for the gene of interest and find not only the chromosome, but by playing a little bit with the zoom level, what are the syntenic genes of interest.
• And/Or you can also take a look by searching the Gene NCBI database (that means enter into NCBI, select the Gene database, and then do the searching), that will provide you with a simpler map with the ligated genes
• If you are interested in obtaining the DNA sequence, you can also look into Biomart