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Edward G. Miner Library

Bioinformatics, Biostatistics and Molecular Biology: Variation in the Normal Genome

European Bioinformatics Institute

The European Bioinformatics Institute is the European node for collecting and disseminating biological data. Some of its tools are: BLAST or FASTA programs for sequence similarity- homology analysis; InterProScan for motifs analysis; ClustalW2 for sequence alignment; MSDfold for protein structure query and comparison.


BioGPS -- A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.


GeneCards®: GeneCards is a searchable, integrated, database of human genes that provides concise genomic related information, on all known and predicted human genes.

NCBI Databases

NCBI Training and Tutorials

Visit NBCI's YouTube channel for a variety of quick tutorials on NCBI resources.

The Training & Tutorials page at NCBI is a great resource from NCBI. It provides information for using NBCI tools, such as databases, downloads, and tools.

ENCODE and Roadmap Epigenome Resources

The ENCODE Portal hosts data and information on Encyclopedia of DNA Elements projects in human, mouse, worm and fly genomes.

The UCSC Genome Bioinformatics Site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to the ENCODE and Neandertal projects.

Factorbook organizes results of ENCODE transcription factor ChIP-seq data, integrated with other ENCODE data such as ChIP-seq of histone marks and nucleosome occupancy.

The NIH Roadmap Epigenomics Mapping Consortium is producing a public resource of human epigenomic data, specifically to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease.

Integrated View of the Genome Literature

ENCODE Project Publications and Collections:

"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project".  The ENCODE Project Consortium, Nature 447, 799-816 (14 June 2007)

Nature ENCODE Portal

Genome Biology ENCODE Portal

"An integrated encyclopedia of DNA elements in the human genome".  The ENCODE Project Consortium, Nature 489: 57-74 (6 Sept 2012).

Related Citations:

"8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage". C.M. Rands et al. PLoS Genet. 10: e1004525, July 2014.