creDB 0.1.9 – Cis–REgulatory elements DataBase

creDB 0.1.9

:: DESCRIPTION

The creDB package provides easy access to a sqlite database containing enhancer sequences annotated across a range of biological contexts (tissues, cell types).

::DEVELOPER

Kostka Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R

:: DOWNLOAD

creDB

:: MORE INFORMATION

Citation

Genome-wide Enhancer Maps Differ Significantly in Genomic Distribution, Evolution, and Function.
ML Benton, SC Talipineni, D Kostka,
JA Capra BMC Genomics 2019.

Pfam 32.0 – A database of Protein Domain Families

Pfam 32.0

:: DESCRIPTION

Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.

:: DEVELOPER

Pfam team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432. doi: 10.1093/nar/gky995.
The Pfam protein families database in 2019.
El-Gebali S et al.

CanProVar 2.0 – Human Cancer Proteome Variation Database

CanProVar 2.0

:: DESCRIPTION

CanProVar is designed to store and display single amino acid alterations including both germline and somatic variations in the human proteome, especially those related to the genesis or development of human cancer based on the published literatures.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation.
Zhang M, Wang B, Xu J, Wang X, Xie L, Zhang B, Li Y, Li J.
J Proteome Res. 2017 Feb 3;16(2):421-432. doi: 10.1021/acs.jproteome.6b00505.

GRAPES 2.9 – SMP Querying system for Efficient Parallel Subgraph Isomorphism in databases of Graphs

GRAPES 2.9

:: DESCRIPTION

GRAPES is a querying system for parallel searching in databases of graphs, and single target graph, using symmetric multiprocessing (SMP) architectures. It implements a parallel version of well established graph searching algorithms providing efficient solutions for graphs indexing and matching.

::DEVELOPER

Alfredo Pulvirenti

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GRAPES

:: MORE INFORMATION

Citation:

GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures.
Giugno R, Bonnici V, Bombieri N, Pulvirenti A, Ferro A, Shasha D.
PLoS One. 2013 Oct 22;8(10):e76911. doi: 10.1371/journal.pone.0076911.

SPIKE – Database of highly curated human Signaling Pathways

SPIKE

:: DESCRIPTION

SPIKE (Signaling Pathways Integrated Knowledge Engine) is a database of highly curated human signaling pathways with an associated interactive software tool.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

SPIKE: a database of highly curated human signaling pathways.
Paz A, Brownstein Z, Ber Y, Bialik S, David E, Sagir D, Ulitsky I, Elkon R, Kimchi A, Avraham KB, Shiloh Y, Shamir R.
Nucleic Acids Res. 2011 Jan;39(Database issue):D793-9. doi: 10.1093/nar/gkq1167.

EhecRegNet v2 – Database of Pathogenic E. coli Transcriptional Gene Regulatory Networks

EhecRegNet v2

:: DESCRIPTION

EhecRegNet is a database of gene regulations conserved between E. coli K12 and human pathogenic EHEC strains.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Integr Biol (Camb). 2012 Jul;4(7):728-33. doi: 10.1039/c2ib00132b.
On the trail of EHEC/EAEC–unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria.
Pauling J1, Röttger R, Neuner A, Salgado H, Collado-Vides J, Kalaghatgi P, Azevedo V, Tauch A, Pühler A, Baumbach J.

Traitpedia – Collaborative Database of Species Traits

Traitpedia

:: DESCRIPTION

Traitpedia is a collaborative repository to gather many traits for an increasing number of species

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Mar 15;35(6):1079-1081. doi: 10.1093/bioinformatics/bty743.
Traitpedia: a collaborative effort to gather species traits.
Mier P, Andrade-Navarro MA.

Nexalign 1.35 – Aligns Sequences to Databases

Nexalign 1.35

:: DESCRIPTION

Nexalign is a program to align millions of short reads from next-generation sequencing data sets to reference genomes.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Nexalign

:: MORE INFORMATION

EdgeExpressDB 0.954 – Integrated database of Promoters, Genes, microRNAs, Expression Dynamics and Regulatory Interactions.

EdgeExpressDB 0.954

:: DESCRIPTION

EdgeExpressDB (eeDB) is a federated data abstraction system designed for integrating, interpreting, and visualizing very large biology datasets.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux
  • Perl DBI/DBD, MySQL, SQLite.

:: DOWNLOAD

 EdgeExpressDB

:: MORE INFORMATION

Citation

Genome Biol. 2009;10(4):R39. doi: 10.1186/gb-2009-10-4-r39. Epub 2009 Apr 19.
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.
Severin J1, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR.

eSNPO – SNP Annotation Database and Enrichment analysis platform

eSNPO

:: DESCRIPTION

eSNPO (eQTL based SNP Ontology) is a SNP annotation database and enrichment analysis platform. GWAS is an examination of many common genetic variants in different individuals to see if any variant is associated with a trait. GWASs typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major diseases. Expression quantitative trait loci (eQTLs) are genomic loci that contribute to variation in expression levels of mRNAs. Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species.

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Sci Rep. 2016 Jul 29;6:30595. doi: 10.1038/srep30595.
eSNPO: An eQTL-based SNP Ontology and SNP functional enrichment analysis platform.
Li J, Wang L, Jiang T, Wang J, Li X, Liu X, Wang C, Teng Z, Zhang R, Lv H, Guo M.