Tag: Database

ARGminer – Antibiotic Resistance Gene Miner database

ARGminer

:: DESCRIPTION

ARGminer is an online resource for the inspection and curation of ARGs based on crowdsourcing as well as a platform to promote interaction and collaboration for the ARG scientific community.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Arango-Argoty GA, Guron GKP, Garner E, Riquelme MV, Heath LS, Pruden A, Vikesland PJ, Zhang L.
ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes.
Bioinformatics. 2020 May 1;36(9):2966-2973. doi: 10.1093/bioinformatics/btaa095. PMID: 32058567.

WebSTR – Population-wide database of short Tandem Repeat Variation in humans

WebSTR

:: DESCRIPTION

WebSTR is a web application for browsing a variety of STR datasets. It is based off of the popular ExAC browser.

::DEVELOPER

Gymrek Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

 

REPIC – A Database for Epitranscriptomics

REPIC

:: DESCRIPTION

REPIC (RNA Epitranscriptome Collection) is a database dedicated to provide a new resource to investigate potential functions and mechanisms of N6-adenosine methylation (m6A) modifications.

::DEVELOPER

Chen Group at U Chicago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Liu S, Zhu A, He C, Chen M.
REPIC: a database for exploring the N6-methyladenosine methylome.
Genome Biol. 2020 Apr 28;21(1):100. doi: 10.1186/s13059-020-02012-4. PMID: 32345346; PMCID: PMC7187508.

TreeFam r9 – Database of Animal Gene Trees

TreeFam r9

:: DESCRIPTION

TreeFam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.

::DEVELOPER

TreeFam team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TreeFam v9: a new website, more species and orthology-on-the-fly.
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A.
Nucleic Acids Res. 2013 Nov 4

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D572-80.
TreeFam: a curated database of phylogenetic trees of animal gene families.
Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R.

Satellog 1.0 – Database of Repeat Prioritization

Satellog 1.0

:: DESCRIPTION

Satellog is a database for the identification and prioritization of satellite repeats in disease association studies.Satellog analyzes each pure repeat in UniGene clusters for evidence of repeat polymorphism.

::DEVELOPER

Satellog team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 Satellog

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2005 Jun 10;6:145.
Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.
Missirlis PI, Mead CL, Butland SL, Ouellette BF, Devon RS, Leavitt BR, Holt RA.

mkdom/Xdom 2 – Build the ProDom Database

mkdom/Xdom 2

:: DESCRIPTION

mkdom is the program we use routinely to build each new release of ProDom, Protein domain families automatically generated from protein databases. It relies on the assumption that the shortest amino acid sequence corresponds to a single domain, and may be used as a query to screen the database with the psi-blast program, in order to cluster homologous domains. For building ProDom, we run this program on the whole swissprot/trembl database, but it can be run on any set of protein sequences (as long as you have a fasta file).

xdom is a graphical program which will help you to analyze domains detected by mkdom2, as it visualises all domain arrangements in the protein set.

::DEVELOPER

the ProDom team 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 mkdom/Xdom

:: MORE INFORMATION

Citation

Gouzy J., Corpet F. & Kahn D. (1999).
Whole genome protein domain analysis using a new method for domain clustering,
Computers and Chemistry. 23:333-340.

GOUZY J., EUGENE P. , GREENE E.A. , KAHN D. 1 and CORPET F.
XDOM, a graphical tool to analyse domain arrangements in any set of protein sequences
Comput Appl Biosci (1997) 13 (6): 601-608.

DASH – Database of Aligned Structural Homologs

DASH

:: DESCRIPTION

DASH is a database of structural alignments for all known structurally homologous protein domains and chains in the PDB.

::DEVELOPER

Department of Genome Informatics; Research Institute for Microbial Diseases; Osaka University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res, 47 (W1), W5-W10 2019 Jul 2
MAFFT-DASH: Integrated Protein Sequence and Structural Alignment
John Rozewicki , Songling Li, Karlou Mar Amada, Daron M Standley, Kazutaka Katoh

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.