STAMP 1.1 – Tool-kit for DNA Motif Comparison

STAMP 1.1

:: DESCRIPTION

STAMP is a newly developed web server that is designed to support the study of DNA-binding motifs. STAMP may be used to query motifs against databases of known motifs; the software aligns input motifs against the chosen database (or alternatively against a user-provided dataset), and lists of the highest-scoring matches are returned. Such similarity-search functionality is expected to facilitate the identification of transcription factors that potentially interact with newly discovered motifs.

:: DEVELOPER

Benos Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 STAMP

:: MORE INFORMATION

Citation:

S Mahony, PV Benos,
STAMP: a web tool for exploring DNA-binding motif similarities“,
Nucleic Acids Research (2007) 35(Web Server issue):W253-W258.

DiPhiSeq 0.2.0 – Robust Comparison of Expression levels

DiPhiSeq 0.2.0

:: DESCRIPTION

DiPhiSeq is an R package of robust tests for differential dispersion and differential expression in RNA-Sequencing Data

::DEVELOPER

Jun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/  Linux / WIndows
  • R Package

:: DOWNLOAD

DiPhiSeq

:: MORE INFORMATION

Citation

Bioinformatics, 35 (13), 2235-2242 2019 Jul 1
DiPhiSeq: Robust Comparison of Expression Levels on RNA-Seq Data With Large Sample Sizes
Jun Li , Alicia T Lamere

UnderII – Regulatory Sequences Comparison

UnderII

:: DESCRIPTION

UnderII is a software of alignment-free comparison of regulatory sequences (cis-regulatory modules).

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 UnderII

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jul-Aug;11(4):628-37. doi: 10.1109/TCBB.2014.2306830.
Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison.
Comin M, Verzotto D.

RRS – Comparison of regulatory DNA Sequences

RRS

:: DESCRIPTION

RRS (Regulatory Region Scoring)  is a new computational framework for the detection of functional conservation of regulatory sequences using predicted occupancy levels of transcription factors of interest.

::DEVELOPER

Dr Sascha Ott

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • C /R

:: DOWNLOAD

 RRS

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Oct 1;26(19):2391-7. doi: 10.1093/bioinformatics/btq453. Epub 2010 Aug 9.
An alignment-free model for comparison of regulatory sequences.
Koohy H1, Dyer NP, Reid JE, Koentges G, Ott S.

STON – Protein 3D Structure Comparison

STON

:: DESCRIPTION

STON is a new algorithm to find aligned residues in two proteins with desired rmsd value.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Comput Biol Med. 2009 Feb;39(2):166-72. doi: 10.1016/j.compbiomed.2008.12.004. Epub 2009 Jan 23.
STON: A novel method for protein three-dimensional structure comparison.
Eslahchi C1, Pezeshk H, Sadeghi M, Massoud Rahimi A, Maboudi Afkham H, Arab S.

CEpBrowser 20150219 – Comparison of Epigenomic Modifications across Species

CEpBrowser 20150219

:: DESCRIPTION

CEpBrowser (Comparative Epigenome Browser) is a gene-centric genome browser that visualize the genomic features of multiple species with color-coded orthologous regions, aiding users in comparative genomic research. The genome browser is adapted from UCSC Genome Browser and the orthologous regions are generated from cross-species lift-over pairs.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 1;29(9):1223-5. doi: 10.1093/bioinformatics/btt114. Epub 2013 Mar 29.
Enabling interspecies epigenomic comparison with CEpBrowser.
Cao X, Zhong S.

D2Z 0.1 – Alignment Free Comparison of Regulatory Sequences

D2Z 0.1

:: DESCRIPTION

D2Z is based on comparing the frequencies of all fixed-length words in the two sequences. An important, novel feature of the score is that it is comparable across sequence pairs drawn from arbitrary background distributions.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

D2Z Source Code

:: MORE INFORMATION

Citation:

A statistical method for alignment-free comparison of regulatory sequences
Miriam R. Kantorovitz,Gene E. Robinson, Saurabh Sinha.
Bioinformatics. 2007 Jul 1;23(13):i249-55.

MaxCluster – Protein Structure Comparison and Clustering

MaxCluster

:: DESCRIPTION

MaxCluster (MaxSub and Clustering) is a command-line tool for the comparison of protein structures. It provides a simple interface for a large number of common structure comparison tasks. A key feature of the program is the ability to process thousands of structures, either against a single reference protein or in an all-verses-all comparison.
::DEVELOPER

Alex Herbert , Structural Bioinformatics Group, Imperial College

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • GCC

:: DOWNLOAD

 MaxCluster

:: MORE INFORMATION

LayerCake 20171023 – Visual Comparison of Viral Deep Sequencing data

LayerCake 20171023

:: DESCRIPTION

LayerCake is a tool created for visualizing viral variation from next generation sequencing data

::DEVELOPER

collaboration between labs associated with UW Computer Sciences andUW Pathology & Laboratory Medicine Departments.

:: SCREENSHOTS

LayerCake

:: REQUIREMENTS

  • Windows / MacOsX
  • Java

:: DOWNLOAD

 LayerCake

:: MORE INFORMATION

Citation

LayerCake: a tool for the visual comparison of viral deep sequencing data.
Correll M, Bailey AL, Sarikaya A, O’Connor DH, Gleicher M.
Bioinformatics. 2015 Jul 7. pii: btv407.