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.

CoevDB – Database of Pair-wise Nucleotide Coevolution

CoevDB

:: DESCRIPTION

CoevDB is a database that collects prediction of coevolution between pairs of sites within DNA coding sequences.

::DEVELOPER

The Computational Phylogenetics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2019 Jan 8;47(D1):D50-D54. doi: 10.1093/nar/gky986.
CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates.
Meyer X, Dib L, Salamin N.

PRIAM 201303 – Sequence Profiles Generated from the ENZYME database

PRIAM 201303

:: DESCRIPTION

PRIAM (PRofils pour l’Identification Automatique du Métabolisme) is a method for automated enzyme detection in a fully sequenced genome, based on all sequences available in the ENZYME database.PRIAM relies on sets of position-specific score matrices (PSSMs) automatically tailored for each ENZYME entry. The whole Swiss-Prot database has been used to parameterise and to assess the method. As an example, PRIAM was applied to predict metabolic pathways from the complete genome of the nitrogen fixing bacterium Sinorhizobium meliloti and on the plant pathogen Ralstonia solanacearum. The results of this automated annotation method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of predicted metabolic pathways and to highlight potentially missing enzymes.

::DEVELOPER

PRIAM Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • Java

:: DOWNLOAD

 PRIAM 

:: MORE INFORMATION

Citation

Clotilde Claudel-Renard, Claude Chevalet, Thomas Faraut and Daniel Kahn
Enzyme-specific profiles for genome annotation: PRIAM
Nucleic Acids Research, 2003, Vol. 31, No. 22 6633-6639

AOD – Antioxidant Protein database

AOD

:: DESCRIPTION

AOD (the antioxidant protein database) is a manually curated database of experimentally validated antioxidant proteins. Information including taxonomy, source organism, subcellular location, gene ontology, catalytic activity and function of antioxidant proteins are all extracted from UniProtKB/Swiss-Prot (release 2016_11) and captured in AOD.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

AOD: the antioxidant protein database.
Feng P, Ding H, Lin H, Chen W.
Sci Rep. 2017 Aug 7;7(1):7449. doi: 10.1038/s41598-017-08115-6.

Hemolytik – Database of Hemolytic and Non-hemolytic Peptides

Hemolytik

:: DESCRIPTION

Hemolytik is a manually curated database of experimentally validated Hemolytic and Non-hemolytic peptides.

::DEVELOPER

Hemolytik team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides.
Gautam A, Chaudhary K, Singh S, Joshi A, Anand P, Tuknait A, Mathur D, Varshney GC, Raghava GP.
Nucleic Acids Res. 2014 Jan;42(Database issue):D444-9. doi: 10.1093/nar/gkt1008.

EGFRIndb – Epidermal Growth Factor Receptor Inhibitor Database

EGFRIndb

:: DESCRIPTION

EGFRIndb is a literature curated database of 4581 small molecule inhibitors that have shown activity against either epidermal growth factor receptor isoforms (EGFR, ErbB2, ErbB4) or mutants of EGFR-TK domain (L858R, T790M, double mutant).

::DEVELOPER

EGFRIndb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

EGFRIndb: epidermal growth factor receptor inhibitor database.
Yadav IS, Singh H, Khan MI, Chaudhury A, Raghava GP, Agarwal SM.
Anticancer Agents Med Chem. 2014;14(7):928-35.

HerceptinR – Database of Herceptin Resistance

HerceptinR

:: DESCRIPTION

HerceptinR is a database of assays performed to test sensitivity or resistance of Herceptin Antibodies towards breast cancer cell lines. This database provides comprehensive information about experimental data perform to understanding factors behind herceptin resistance aas well as assays peformed for improving Herceptin sensitivity with the help of supplementary drugs.

::DEVELOPER

HerceptinR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Herceptin resistance database for understanding mechanism of resistance in breast cancer patients.
Ahmad S, Gupta S, Kumar R, Varshney GC, Raghava GP.
Sci Rep. 2014 Mar 27;4:4483. doi: 10.1038/srep04483.

ParaPep – Database of Anti-parasitic peptides

ParaPep

:: DESCRIPTION

ParaPep is a manually curated repository of experimentally validated anti-parasitic peptides and their structures. Data have been collected from research papers, published patents and other databases.

::DEVELOPER

ParaPep team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and their structures.
Mehta D, Anand P, Kumar V, Joshi A, Mathur D, Singh S, Tuknait A, Chaudhary K, Gautam SK, Gautam A, Varshney GC, Raghava GP.
Database (Oxford). 2014 Jun 12;2014. pii: bau051. doi: 10.1093/database/bau051.

CancerPPD – Database of Anticancer Peptides and Proteins

CancerPPD

:: DESCRIPTION

CancerPPD is a unique resource of its kind, which provides detailed information related to experimentally verified anticancer peptides (ACPs) and proteins.

::DEVELOPER

CancerPPD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CancerPPD: a database of anticancer peptides and proteins.
Tyagi A, Tuknait A, Anand P, Gupta S, Sharma M, Mathur D, Joshi A, Singh S, Gautam A, Raghava GP.
Nucleic Acids Res. 2015 Jan;43(Database issue):D837-43. doi: 10.1093/nar/gku892.

AHTPDB – Anti Hypertensive Inhibiting peptide database

AHTPDB

:: DESCRIPTION

AHTPDB is a manually curated database of experimentally validated antihypertensive peptides.

::DEVELOPER

AHTPDB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

AHTPDB: a comprehensive platform for analysis and presentation of antihypertensive peptides.
Kumar R, Chaudhary K, Sharma M, Nagpal G, Chauhan JS, Singh S, Gautam A, Raghava GP.
Nucleic Acids Res. 2015 Jan;43(Database issue):D956-62. doi: 10.1093/nar/gku1141.