ElemeNT Ver 2 – Tool for Detection of core Promoter Elements

ElemeNT Ver 2

:: DESCRIPTION

ElemeNT (Elements Navigation Tool) is an interactive tool for rapid and convenient detection of core promoter elements within a given sequence, implemented in Perl programming language.

::DEVELOPER

Juven-Gershon Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Transcription. 2015;6(3):41-50. doi: 10.1080/21541264.2015.1067286.
ElemeNT: a computational tool for detecting core promoter elements.
Sloutskin A, Danino YM, Orenstein Y, Zehavi Y, Doniger T, Shamir R, Juven-Gershon T.

PINES – Phenotype-Informed Noncoding Element Scoring

PINES

:: DESCRIPTION

PINES evaluates the functional impact of noncoding variants by integrating diverse epigenetic annotations, utilizing genomic annotations most relevant to phenotypes of interest.

::DEVELOPER

SUNYAEV LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • R

:: DOWNLOAD

PINES

:: MORE INFORMATION

Citation

Bodea CA, Mitchell AA, Bloemendal A, Day-Williams AG, Runz H, Sunyaev SR.
PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants.
Genome Biol. 2018 Oct 25;19(1):173. doi: 10.1186/s13059-018-1546-6. PMID: 30359302; PMCID: PMC6203199.

Kalzium 21.08.0 – Periodic Table of Elements

Kalzium 21.08.0

:: DESCRIPTION

Kalzium is your digital replacement for the periodic table on paper. It is a program that visualizes the Periodic Table of Elements (PSE) and includes basic information about all common elements in the PSE. It has a gained much more functions over time.

::DEVELOPER

Kalzium Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Complier

:: DOWNLOAD

 Kalzium

:: MORE INFORMATION

Logopaint 1.0 – Exploring Visualisation of Bias in Regulatory DNA or RNA Element

Logopaint 1.0

:: DESCRIPTION

Logopaint is a software of exploring the visualisation of bias in regulatory DNA or RNA element, using information context and modified logos.

::DEVELOPER

Dr Chris Brown’s Research Group

:: SCREENSHOTS

Logopaint

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

 Logopaint

:: MORE INFORMATION

Citation:

Bioinformatics. 2002 Apr;18(4):507-12.
Compensation for nucleotide bias in a genome by representation as a discrete channel with noise.
Schreiber M1, Brown C.

Cis-regPred – Cis-regulatory Element Predictor

Cis-regPred

:: DESCRIPTION

Cis-regPred predicts intrinsically disordered protein regions that may regulate protein function by mediating interactions in cis.

::DEVELOPER

Gsponer Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Yeon JH, Heinkel F, Sung M, Na D, Gsponer J.
Systems-wide Identification of cis-Regulatory Elements in Proteins.
Cell Syst. 2016 Feb 24;2(2):89-100. doi: 10.1016/j.cels.2016.02.004. Epub 2016 Feb 24. PMID: 27135163.

Element 2.0 – Identify Over-represented Motifs across groups of Promoters

Element 2.0

:: DESCRIPTION

Element is a web-based tool that identifies over-represented motifs across groups of promoters. Numerous plant genomes are already available online to be run against. If you don’t see your genome of interest, feel free to suggest that we add it.

::DEVELOPER

Mockler Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.
Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J.
Cold Spring Harb Symp Quant Biol. 2007;72:353-63. doi: 10.1101/sqb.2007.72.006.

RNAAnalyzer – Identify Regulatory RNA Elements

RNAAnalyzer

:: DESCRIPTION

RNAAnalyzer is an integrated tool-box to identify regulatory RNA elements. The RNA analyzer collects general and specific information on any submitted RNA sequence or batch of sequences in FASTA format. It determines and rapidly scans the different regions of an RNA (including 5′ UTR, CDS, 3′ UTR in mRNA) and screens for specific RNA signals (in each of these regions, e.g. polyA-site, AU rich region etc. in 3′ UTR). It runs a fast folding RNA routine to provide an overview of the RNA fold. Furthermore it analyzes structure content, fold energy and stem loops.

::DEVELOPER

the Department of Bioinformatics at the University of Würzburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Peter Bengert and Thomas Dandekar
A software tool-box for analysis of regulatory RNA elements
Nucl. Acids. Res. 2003 31: 3441-3445.

PALSSE 20090521 – Predictive Assignment of Linear Secondary Structure Elements

PALSSE 20090521

:: DESCRIPTION

PALSSE (Predictive Assignment of Linear Secondary Structure Elements) is a software that delineates secondary structure elements (SSEs) from protein Cα coordinates and specifically addresses the requirements of vector-based protein similarity searches. Our program identifies two types of secondary structures: helix and β-strand, typically those that can be well approximated by vectors. In contrast to traditional secondary structure algorithms, which identify a secondary structure state for every residue in a protein chain, our program attributes residues to linear SSEs. Consecutive elements may overlap, thus allowing residues located at the overlapping region to have more than one secondary structure type.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • python

:: DOWNLOAD

 PALSSE

:: MORE INFORMATION

Citation:

PALSSE: A program to delineate linear secondary structural elements from protein structures
Indranee Majumdar, S Sri Krishna and Nick V Grishin
BMC Bioinformatics 2005, 6:202