I am interested in all variants of a human protein for normal person. I know their is a 1000 human genome project http://www.1000genomes.org/ but I am unable to extract 1000 variants of a protein.
This project provides processed data where they mention SNP/variant in each sequence but I am looking for raw data for each variant of a protein.
Sir, do you want variants of a single protein or multiple ones ? If single then the NCBI GI accession of that protein will be helpful to us to find its variants.
I need variants for single protein, as 1000 human genome sequence project suppose to sequence genome 1000 human. I am looking for 1000 sequences (variants) each correspond to a individual human. This way for single protein I may see variation among 1000 humans.
I think following link will work for you.
Search your gene, and then look for its variants.
If you can provide me the NCBI GI, then I can search it also.
http://browser.1000genomes.org/index.html
Dear Gajendra:
I think these papers can help you:
1)Science. 2012 Feb 17;335(6070):823-8. doi: 10.1126/science.1215040.
A systematic survey of loss-of-function variants in human protein-coding genes.
MacArthur DG,et al.
Nature. 2013 Jan 10;493(7431):216-20. doi: 10.1038/nature11690. Epub 2012 Nov 28.
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.
2)Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ; NHLBI Exome Sequencing Project, Akey JM. Collaborators (396)
Author information
Erratum in
Nature. 2013 Mar 14;495(7440):270. Rieder, Mark J [added].
Abstract
Establishing the age of each mutation segregating in contemporary human populations is important to fully understand our evolutionary history and will help to facilitate the development of new approaches for disease-gene discovery. Large-scale surveys of human genetic variation have reported signatures of recent explosive population growth, notable for an excess of rare genetic variants, suggesting that many mutations arose recently. To more quantitatively assess the distribution of mutation ages, we resequenced 15,336 genes in 6,515 individuals of European American and African American ancestry and inferred the age of 1,146,401 autosomal single nucleotide variants (SNVs). We estimate that approximately 73% of all protein-coding SNVs and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000-10,000 years. The average age of deleterious SNVs varied significantly across molecular pathways, and disease genes contained a significantly higher proportion of recently arisen deleterious SNVs than other genes. Furthermore, European Americans had an excess of deleterious variants in essential and Mendelian disease genes compared to African Americans, consistent with weaker purifying selection due to the Out-of-Africa dispersal. Our results better delimit the historical details of human protein-coding variation, show the profound effect of recent human history on the burden of deleterious SNVs segregating in contemporary populations, and provide important practical information that can be used to prioritize variants in disease-gene discovery
You may want to have a look at the new human 1000 Genomes Project variants file provided by UniProt:
http://www.uniprot.org/news/2013/12/11/release
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/variants/
The human variome project has the one. Else inferring through genetic variation from usegalaxy.org is the best.
I hope this helps.
Regards
Prash
Hi Gajendra,
When you say: "This project provides processed data where they mention SNP/variant in each sequence but I am looking for raw data for each variant of a protein.", I assume you mean that 1000G provides summary information per variant, such as allele frequency, etc, and that what you would like is to have the genotypes per individual for this variant (or potentially all variants for a particular gene).
If this is the case, then your best bet to access the "raw" data (not really raw data as in signal intensities or sequence reads), is to access the VCF files, which stores for all SNPs on a chromosome the genotypes across all individuals.
You can access the 1000G VCF files here:
http://www.1000genomes.org/data
To manipulate VCF format, such as fetching SNP within an interval, such as a gene, use VCF tools:
http://vcftools.sourceforge.net/
You may also be able to fetch genotypes for a gene of interest from one of the browsers that house 1000G data but I am unaware of how to do so:
http://www.1000genomes.org/1000-genomes-browsers
Hope this helps,
Vince
Hello all,
Dr. Raghava want to find out the variants of all genes in each organism (i.e. Human) of 1000 genome project. So, we need organism wise list of variations.
I am doing it by downloading .vcf files of each chromosome from the link
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/ .
After this, we can extract vcf file for each individual (i.e. human) of 1000 genome from vcf file of each chromosome by the command (suppose for chromosome 16)
tabix -h ALL.chr16.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz
16:1-90354753 | perl vcftools_0.1.11/bin/vcf-subset -c sample-name | tabix-0.2.6/bgzip -c >sample.vcf.gz
We will get 23X1000 vcf files from this. Afterwords, we will process the VCF files with ANNOVAR, to map the variants on genes and .fasta sequence of 1000 genes can be made.
According to me,this may be the possible solution of this. Please correct me, if i am at different path.
Any suggestion is highly appreciated.
Regards
SHAILESH KUMAR
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics