This is a brief description of web services, which are intensively used for 3D Genome Browser and also may be used for retrieving data of human genome in 3 dimensional space.
This web service provides an access to the 3D structure of different models. Currently, there are three models of human 3D genome structures. The structures are interpolated with a finite number of points. The volume encompassing the genome structure is segmented in 3D cubic cells. Spatial queries use the coordinates of a cube (starting and ending positions on the x, y, and z axis) as an input, and return the coordinates of the interpolation points modelling the DNA chains contained within this cell. In particular, it allows us to identify the ranges of DNA subsequences within this volume.
Example could be:
http://1kgenome.exascale.info/3d?chr=19&m=normal&xstart=2&xend=3&ystart=2¥d=3&zstart=2&zend=3
Fill the following fields to have an appropriate example of the command.
Get 3D structure for cubic area in range X: from to , Y: from to , Z: from to ,
using healthy, leukemia or simulated cell data, for chromosome .
This web-service provides an access to the Nucleotide sequences from GRCh38 asembly of the human genome from the UCSC genome browser. In the 3DGB it is used as a reference genome sequence. Nucleotide sequences can be accessed from their chromosomic location.
Example could be:
http://1kgenome.exascale.info/range?chrid=1&start=59146954&end=59148000
Fill the following fields to have an appropriate example of the URL.
Get Nucleotide data for chromosome in range(positions) from to .
This web-service provides an access to the storage of the Single Nucleotide Polymorphism (SNP) data from the 1000 Genomes Project. A query returns an array of arrays showing information for each individual SNP found within this interval. This information is represented as a 4-tuple including the SNP position, the SNP ID and the two alleles.
Example could be:
http://1kgenome.exascale.info/js_snp?chr=1&start=59146954&end=59148000
Fill the following fields to have an appropriate example of the URL.
Get SNPs information data for chromosome in range(positions) from to .
This web-service provides an access to the experimental ChIP-sequencing data from the ENCODE project stored in UCSC genome browser. This data is usefull for identifying transcription factors binding sites(TFBS). The output of such query is an array of 7-tuples that contain basic information on the Chip-Seq data. A 7-tuple stores the chromosome number, starting and ending index of the Chip-Seq peak, the transcription factor name, a normalized value (ranging from 1 to 1000) indicating the magnitude of the binding, the cell lines with similar TFBS, and a list of SNPs occurring in this binding site.
Example could be:
http://1kgenome.exascale.info/chipseq?chr=1&start=59146954&end=59160000
Fill the following fields to have an appropriate example of the URL.
Get ChIP-Sequencing data for chromosome in range(positions) from to for specific Cell Line
.
As spatial data is presented as a finite set of points in 3D space, this web-service provides the closest in terms of strand existing point in the database. This service is usefull for approximation of the data, alligning data from different resources.
Example could be:
http://1kgenome.exascale.info/chipseq?chr=1&start=59146954&end=59160000
Fill the following fields to have an appropriate example of the URL.
Find the closest point in 3DGB database to the point on chromosome position ;
using healthy, leukemia or simulated cell data