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Table 1 Data and analysis tools (open-source)

From: Identification of cis-regulatory sequence variations in individual genome sequences

Genetic variant data

 

dbSNP

http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/projects/SNP/

 

1000 Genomes

http://www.1000genomes.org/

 

HapMap Project

http://hapmap.ncbi.nlm.nih.gov/

Coding variant characterization

 

SIFT

http://sift.jcvi.org/

 

Polyphen-2

http://genetics.bwh.harvard.edu/pph2/

ChIP-Seq data

 

Gene Expression Omnibus (GEO)

http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/geo/

 

ENCODE project

http://genome.ucsc.edu/ENCODE/

 

PAZAR

http://www.pazar.info/

Motif discovery

 

Meme-ChIP

http://meme.nbcr.net/

TFBS profiles

 

JASPAR

http://jaspar.genereg.net/

 

PAZAR

http://www.pazar.info/

TFBS databases

 

PAZAR

http://www.pazar.info/

 

ORegAnno

http://www.oreganno.org/

TFBS variant characterization

 

Variant effect predictor

http://uswest.ensembl.org/tools.html

 

is-rSNP

http://www.genomics.csse.unimelb.edu.au/is-rSNP/

 

rSNP-MAPPER

http://genome.ufl.edu/mapper/

RNA-Seq splice analysis

 

TopHat

http://tophat.cbcb.umd.edu/

 

MapSplice

http://www.netlab.uky.edu/p/bioinfo/MapSplice

Splice enhancer discrimination

 

SFmap

http://sfmap.technion.ac.il/

 

ESE Finder

http://rulai.cshl.edu/tools/ESE

Data management and visualization

 

Galaxy (tool kit)

http://galaxy.psu.edu/

 

UCSC Genome Browser

http://genome.ucsc.edu/

 

Ensembl BioMart

http://www.ensembl.org/biomart/martview/