Dear Friends, I want to download the entire human gene list with the information about their chromosomal location, i.e. that specific gene is present in which chromosome and which arm (p or q). Is there any specific databases to give such an information, please guide me. Thanking in advance for the replies.
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arulthasan83cyr •
Just use Biomart. Using the Ensembl annotation, you can get a list of Ensembl IDs, the associated gene names, chromosome, position, and band (such as p22.1). You can also filter the results for the exact type of gene (known, novel, etc.) you want.
Edit: FYI, if you just want the actual coordinates instead, just download a GTF file or follow one of the other answers.
My suggestion would be Gencode genes (version 18 - 57445 human genes).
Annotation is in base pairs (much more accurate than chromosome arms).
All you have to do is:
curl -s "ftp://ftp.sanger.ac.uk/pub/gencode/release_18/gencode.v18.annotation.gtf.gz" |
gunzip -c > Human_genes.gtf
It's in GTF format.
mkosinski@mkosinski-E540:~$ curl -s "ftp://ftp.sanger.ac.uk/pub/gencode/release_18/gencode.v18.annotation.gtf.gz" | gunzip -c > Human_genes.gtf
gzip: stdin: unexpected end of file
The half life of a link in bioinformatics is just a few months. It looks like this has moved to "ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_18/gencode.v18.annotation.gtf.gz". You may as well check for a newer release. As of March 28 2017, it seems that release 26 is the most up to date.
There are several places which provide databases on human gene annotation for download.
Try the Ensembl databases (http://www.ensembl.org/downloads.html) or data from the UCSC genome browser (http://hgdownload.soe.ucsc.edu/downloads.html#human) for example.
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