What's a KnownGene file?

Question

[Bairon Hernández]

Hello everybody,

i'm new in this website, i study bioinformatics in Chile. Well, my question is: what's a knownGene file and what's difference have with GFF/GTF file?. I know about the format file is difference, but i ask about the information that have each one.

Thanks so much for your time :D

[GenoMax]

I guess you are referring to knownGene file from UCSC. It will have information about gene identifiers used by UCSC and their mapping on the genome. GFF/GTF file will have similar information using HGNC gene names (in case of human gene).

Answer 1

[sbwiecko]

It's a kind of GenePred table concatenated with

1. the proteinID from UniProt or RefSeq, and
2. the alignID from GENCODE.