Tag: Location

iDHS-EL – Identifying the location of DHS in human Genome

iDHS-EL

:: DESCRIPTION

iDHS-EL is a webserver of identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Liu B, Long R, Chou KC.
iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework.
Bioinformatics. 2016 Aug 15;32(16):2411-8. doi: 10.1093/bioinformatics/btw186. Epub 2016 Apr 8. PMID: 27153623.

CSDeconv 1.03 – Determine Locations of Transcription Factor Binding from ChIP-seq data

CSDeconv 1.03

:: DESCRIPTION

CSDeconv maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach

::DEVELOPER

Desmond Lun

:: SCREENSHOTS

N/a

::REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 CSDeconv

:: MORE INFORMATION

Citation

D. S. Lun, A. Sherrid, B. Weiner, D. R. Sherman, and J. E. Galagan.
A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-Seq data.
Genome Biol., 10(12):R142, December 2009.

MOLE 2.5 – Location and Characterization of Channels, Tunnels and Pores in Molecular Structures

MOLE 2.5

:: DESCRIPTION

Program MOLE is an universal toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in molecular structures. The core of MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. MOLE is a powerful software (overcomming some limitations of CAVER tool) for exploring large molecular channels, complex networks of channels and molecular dynamics trajectories (AMBER ascii traj and parm7 are supported) in which analysis of a large number of snapshots is required.

::DEVELOPER

Martin Petrek (NCBR), Michal Otyepka (FCH UPOL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

MOLE

:: MORE INFORMATION

Citation:

Structure. 2007 Nov;15(11):1357-63.
MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels.
Petrek M, Kosinová P, Koca J, Otyepka M.

FlaiMapper 3.0.0 – Fragment Location Annotation Identification Mapper

FlaiMapper 3.0.0

:: DESCRIPTION

FlaiMapper is a method that extracts and annotates the locations of sncRNA-derived RNAs (sncdRNAs).

::DEVELOPER

FlaiMapper team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FlaiMapper

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 22. pii: btu696.
FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data.
Hoogstrate Y, Jenster G, Martens-Uzunova ES

TFM-Scan – Efficient Location of Position Weight Matrices on a DNA sequence

TFM-Scan

:: DESCRIPTION

TFM-Scan is a program dedicated to the location of large sets of putative transcription factor binding sites on a DNA sequence.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • C++ Compiler

 TFM-Scan

:: MORE INFORMATION

Citation

Large scale matching for Position Weight Matrices
Liefooghe A., Touzet H. and Varré J.-S.
In Combinatorial Pattern Matching, volume 4009 of Lecture Notes in Computer Science, pages 401-412. Springer Verlag, 2006.

BioAtlas – Location-specific analysis of Microbial profiles

BioAtlas

:: DESCRIPTION

BioAtlas is a web service, primarily designed for biologists to explore where 16S rRNA strains classified from bacteria and/or archaea taxonomy are found, whether it be geographical and/or host-oriented locations.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Interactive microbial distribution analysis using BioAtlas.
Lund JB, List M, Baumbach J.
Nucleic Acids Res. 2017 Jul 3;45(W1):W509-W513. doi: 10.1093/nar/gkx304.

subGolgi v2.0 – Prediction of subGolgi locations of Proteins

subGolgi v2.0

:: DESCRIPTION

subGolgi is a sequence-based predictor for identifying Golgi-resident proteins and their types

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Protein Pept Lett. 2011 Jan;18(1):58-63.
Identify Golgi protein types with modified Mahalanobis discriminant algorithm and pseudo amino acid composition.
Ding H1, Liu L, Guo FB, Huang J, Lin H.

SweepFinder 20060814 – Detect the Location of a selective Sweep based on SNP data

SweepFinder 20060814

:: DESCRIPTION

SweepFinder is a program used to detect the location of a selective sweep based on SNP data. It will also estimate the frequency spectrum of observed SNP data in the presence of missing data.

::DEVELOPER

the Nielsen group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SweepFinder

:: MORE INFORMATION

Citation:

Nielsen et al. 2005.
Genomic scans for selective sweeps using SNP data.
Genome Research 1566-1575.

TweenMotif 1.1 – Visualize Locations of a Specified Target Motif

TweenMotif 1.1

:: DESCRIPTION

TweenMotif is an interactive Windows program for visualizing the locations of a specified target motif within a set of sequences, as well as the gaps between the repeating motifs. The program creates a summary table of the frequency counts of the gap sequences that can be pasted into an Excel spreadsheet for further analysis

::DEVELOPER

Earl F Glynn

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

   TweenMotif, Source Code

:: MORE INFORMATION