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.

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.