What Is The Index Of The First Base In Pph2 ? 0 Or 1 ?

Question

[Pierre Lindenbaum]

Dear lazyweb, what is the index of the first base in the genome for "PolyPhen-2-Batch Query"? Is it 0 or 1?

Thanks

Pierre

[Neilfws]

Do you mean "in their database" or "when using the web interface"? The UCSC database is 0-based, but the web user is unaware of that because the web front-end converts to 1-based. I would guess that you enter 1-based queries in the form.

[Pierre Lindenbaum]

Neil, I meant "when using the web interface"

Answer 1

[Bamyasi]

Hi guys!

PPH2 accepts one-based coordinates in user input web form, similar to UCSC, which always uses 1-based coordinate system in their web interface, even though zero-based system is used throughout the underlying database.

Hope this helps.

Ivan Adzhubei

[Hanif Khalak]

Thanks Ivan for the definitive answer since you maintain PPH2!

Answer 2

[Hanif Khalak]

PolyPhen uses the same assemblies as UCSC, and according to the UCSC FAQ explanation, the UCSC internal database coordinates are zero-based, so I'd say the first base is a 0.

[Pierre Lindenbaum]

Thanks, but that is not a proof that PPH2 use an index of 0....