finding homologs in human

Question

[cillekopp]

Hello biostars,

Im new in bioinformatics, and I want to prepare a list of the 6 most similar human homologs of TMPRSS3, which potentially could be off target for drugs targeted against TMPRSS3. I need to Use HGNC symbols in the list.

What is the best way to go about this?

kind regards

Answer 1

[Titus]

Hi,

If you get the fasta (ACGT sequence of your gene) sequence you can make blast in NCBI for exemple and get some similar genes/domains of your protein.

Best

Tristan

[cillekopp]

thx so much - I did exactly that, just with a protein seq.

Do you by any chance know, where I find the HGNC values?

[Titus]

What is HGNC values ? Do you mean id of the gene ?

[cillekopp]

sorry HGNC Symbols ;)

[Titus]

Can you show me a screen shot of your result or the NCBI link ? When you blast you sequences there is a list of best matches with your sequence and if i remember well the gene name symbol is write somewhere ;)

Answer 2

[cillekopp]

https://blast.ncbi.nlm.nih.gov/Blast.cgi#alnHdr_365813088

[Titus]

In description part (under the graphic summary) you have the protein description and the symbol if it exists.