dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions

People from the "Human Genetics Center" in Houston have compiled a new resource named dbNSFP and described in http://www.ncbi.nlm.nih.gov/pubmed/21520341.

Hum Mutat. 2011 Apr 21. doi:10.1002/humu.21517.
dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions.
Liu X, Jian X, Boerwinkle E.

They have compiled the "prediction scores from four new and popular algorithms (SIFT, Polyphen2, LRT and MutationTaster), along with a conservation score (PhyloP) and other related information, for every potential NS in the human genome (a total of 75,931,005)." .

So, you don't have to send some new jobs to SIFT or Polyphen. Everything has already been calculated and joined here.

The database is available from http://sites.google.com/site/jpopgen/dbNSFP.

Downloading

lindenb@yokofakun:~$ wget "http://dl.dropbox.com/u/17001647/dbNSFP/dbNSFP.chr1-22XY.zip"
--2011-04-27 13:50:26-- http://dl.dropbox.com/u/17001647/dbNSFP/dbNSFP.chr1-22XY.zip
Proxy request sent, awaiting response... 200 OK
Length: 1200703405 (1.1G) [application/zip]
Saving to: `dbNSFP.chr1-22XY.zip'

100%[=================================================================================================================>] 1,200,703,405 1.82M/s in 10m 11s

2011-04-27 14:00:38 (1.87 MB/s) - `dbNSFP.chr1-22XY.zip' saved [1200703405/1200703405]

Content

unzip -t dbNSFP.chr1-22XY.zip
Archive: dbNSFP.chr1-22XY.zip
testing: dbNSFP.chr1 OK
testing: dbNSFP.chr10 OK
testing: dbNSFP.chr11 OK
testing: dbNSFP.chr12 OK
testing: dbNSFP.chr13 OK
testing: dbNSFP.chr14 OK
testing: dbNSFP.chr15 OK
testing: dbNSFP.chr16 OK
testing: dbNSFP.chr17 OK
testing: dbNSFP.chr18 OK
testing: dbNSFP.chr19 OK
testing: dbNSFP.chr2 OK
testing: dbNSFP.chr20 OK
testing: dbNSFP.chr21 OK
testing: dbNSFP.chr22 OK
testing: dbNSFP.chr3 OK
testing: dbNSFP.chr4 OK
testing: dbNSFP.chr5 OK
testing: dbNSFP.chr6 OK
testing: dbNSFP.chr7 OK
testing: dbNSFP.chr8 OK
testing: dbNSFP.chr9 OK
testing: dbNSFP.chrX OK
testing: dbNSFP.chrY OK

Sample (verticalized)

>>2
$1 #chr : 22
$2 pos(1-based) : 15453440
$3 ref : T
$4 alt : G
$5 aaref : M
$6 aaalt : L
$7 hg19pos(1-based) : 17073440
$8 genename : CCT8L2
$9 geneid : 150160
$10 CCDSid : CCDS13738.1
$11 refcodon : ATG
$12 codonpos : 1
$13 fold-degenerate : 0
$14 aapos : 1
$15 cds_strand : -
$16 LRT_Omega : 1.116940
$17 PhyloP_score : 0.963611
$18 PlyloP_pred : C
$19 SIFT_score : 1.0
$20 SIFT_pred : D
$21 Polyphen2_score : 0.25
$22 Polyphen2_pred : P
$23 LRT_score : 0.419288
$24 LRT_pred : U
$25 MutationTaster_score : 1.0
$26 MutationTaster_pred : D
<<2
>>3
$1 #chr : 22
$2 pos(1-based) : 15453440
$3 ref : T
$4 alt : C
$5 aaref : M
$6 aaalt : V
$7 hg19pos(1-based) : 17073440
$8 genename : CCT8L2
$9 geneid : 150160
$10 CCDSid : CCDS13738.1
$11 refcodon : ATG
$12 codonpos : 1
$13 fold-degenerate : 0
$14 aapos : 1
$15 cds_strand : -
$16 LRT_Omega : 1.116940
$17 PhyloP_score : 0.963611
$18 PlyloP_pred : C
$19 SIFT_score : 1.0
$20 SIFT_pred : D
$21 Polyphen2_score : 0.25
$22 Polyphen2_pred : P
$23 LRT_score : 0.419288
$24 LRT_pred : U
$25 MutationTaster_score : 1.0
$26 MutationTaster_pred : D
<<3

That's it,

Pierre