Tag: Investigation

ELM / iELM 1.0 – Investigation of Functional Sites in Protein Sequences with Eukaryotic Linear Motif database

ELM / iELM 1.0

:: DESCRIPTION

The ELM (Eukaryotic Linear Motif) resource  provides the biological community with a comprehensive database of known experimentally validated motifs, and an exploratory tool to discover putative linear motifs in user-submitted protein sequences.

The iELM (interactions of Eukaryotic Linear Motif) web server provides a resource for predicting the function and positional interface for a subset of interactions mediated by short linear motifs (SLiMs).

::DEVELOPER

Gibson Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Holger Dinkel et al.
ELM — the database of eukaryotic linear motifs
Nucl. Acids Res. (2012) 40 (D1): D242-D251.

iELM – a web server to explore short linear motif-mediated interactions.
Weatheritt RJ, Jehl P, Dinkel H, Gibson TJ. (2012).
Nucleic Acids Res. 2012 Jul

GenomeVIP v1.2.1 – Cloud based Genome Variant Investigation Platform

GenomeVIP v1.2.1

:: DESCRIPTION

GenomeVIP is a web application platform for performing variant discovery on Amazon’s Web Service (AWS) cloud or on local high-performance computing clusters.

::DEVELOPER

Ding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GenomeVIP

:: MORE INFORMATION

Citation

Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Feny? D, Raphael BJ, Wendl MC, Ding L.
GenomeVIP: a cloud platform for genomic variant discovery and interpretation.
Genome Res. 2017 Aug;27(8):1450-1459. doi: 10.1101/gr.211656.116. Epub 2017 May 18. PMID: 28522612; PMCID: PMC5538560.

LEMMI – Live Evaluation of Computational Methods for Metagenome Investigation

LEMMI

:: DESCRIPTION

LEMMI is the first-of-its-kind continuous benchmarking platform for metagenomics classifiers, featuring multi-objective ranking, and effective distribution of containerised software.

::DEVELOPER

Prof Zdobnov Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Seppey M, Manni M, Zdobnov EM.
LEMMI: a continuous benchmarking platform for metagenomics classifiers.
Genome Res. 2020 Aug;30(8):1208-1216. doi: 10.1101/gr.260398.119. Epub 2020 Jul 2. PMID: 32616517; PMCID: PMC7462069.

PLATINUM – Protein–Ligand ATtractions Investigation NUMerically

PLATINUM

:: DESCRIPTION

PLATINUM is designed for calculation of hydrophobic properties of molecules and their match or mismatch in receptor–ligand complexes

::DEVELOPER

Laboratory of biomolecular modeling.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2009 May 1;25(9):1201-2. doi: 10.1093/bioinformatics/btp111. Epub 2009 Feb 25.
PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes.
Pyrkov TV1, Chugunov AO, Krylov NA, Nolde DE, Efremov RG.

StemCellNet 1.3.3 – Network-oriented Investigations in Stem Cell Biology

StemCellNet 1.3.3

:: DESCRIPTION

StemCellNet is an interactive platform for retrieval and analysis of molecular networks associated with stem cells and their marker genes. It contains a large number of physical and regulatory interactions both from human and mouse, which can be queried by the user through the input of a set of gene or protein identifiers.

::DEVELOPER

Systems Biology and Bioinformatics Laboratory @ University of Algarve

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

StemCellNet: an interactive platform for network-oriented investigations in stem cell biology.
Pinto JP, Reddy Kalathur RK, R Machado RS, Xavier JM, Bragan?a J, Futschik ME.
Nucleic Acids Res. 2014 May 22. pii: gku455.

SciRoKo 3.4 / SciRoKoCo – Whole Genome Microsatellite Search and Investigation / SSR-search module.

SciRoKo 3.4

:: DESCRIPTION

SciRoKo allows for whole genome microsatellite search and investigation. For example, the whole rice genome may be searched in 55 sec. The integrated microsatellite statistics capabilities makes SciRoKo an powerful tool for comparative genomics.

SciRoKoCo is the command line version for the SciRoKo SSR-search module.

::DEVELOPER

Robert Kofler

:: SCREENSHOTS

SciRoKo

:: REQUIREMENTS

  • Linux / WIndows / MacOsX

:: DOWNLOAD

 SciRoKo

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Jul 1;23(13):1683-5. Epub 2007 Apr 26.
SciRoKo: a new tool for whole genome microsatellite search and investigation.
Kofler R, Schlötterer C, Lelley T.