CRISPRmap 2.1- CRISPR Repeat Conservation and Diversity Analysis

CRISPRmap 2.1

:: DESCRIPTION

CRISPRmap provides a quick and detailed insight into repeat conservation and diversity of both bacterial and archaeal systems. It comprises the largest dataset of CRISPRs to date and enables comprehensive independent clustering analyses to determine conserved sequence families, potential structure motifs for endoribonucleases, and evolutionary relationships.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci.
Alkhnbashi OS, Costa F, Shah SA, Garrett RA, Saunders SJ, Backofen R.
Bioinformatics. 2014 Sep 1;30(17):i489-i496. doi: 10.1093/bioinformatics/btu459.

Nucleic Acids Res. 2013 Sep;41(17):8034-44. doi: 10.1093/nar/gkt606. Epub 2013 Jul 17.
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems.
Lange SJ1, Alkhnbashi OS, Rose D, Will S, Backofen R.

FastEP – Fast Computation of Entropic Profiles for the Detection of Conservation in Genomes

FastEP

:: DESCRIPTION

FastEP (Fast Entropic Profiler) is a linear time linear space algorithm suitable for large genomes and for the discovery of motifs with unbounded length.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 FastEP

:: MORE INFORMATION

Citation

M. Antonello, M. Comin,
Fast Computation of Entropic Profiles for the Detection of Conservation in Genomes“,
Proceedings of Pattern Recognition in Bioinformatics 2013,
Lecture Notes in BIoinformatics (LNBI) 2013, 7986, pp. 277–288.

MSARi – Detecting Conservation of RNA Secondary Structure

MSARi

:: DESCRIPTION

The MSARi (Multiple Sequence Alignments for Statistical Detection of RNA Secondary Structure) program indentifies conserved RNA secondary structure in non-coding RNA genes and mRNAs by searching multiple sequence alignments of a large set of candidate catalogs for correlated arrangements of reverse-complementary regions

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 MSARi

:: MORE INFORMATION

Citation:

Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12102-7. Epub 2004 Aug 10.
MSARI: multiple sequence alignments for statistical detection of RNA secondary structure.
Coventry A, Kleitman DJ, Berger B.

OrthoGNC 3.0 – Accurate Identification of Orthologs based on Gene Neighborhood Conservation

OrthoGNC 3.0

:: DESCRIPTION

OrthoGNC is a software for predicting accurate pairwise orthology relations based on gene neighborhood conservation.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Java

:: DOWNLOAD

OrthoGNC

:: MORE INFORMATION

Citation

Genomics Proteomics Bioinformatics. 2017 Dec;15(6):361-370. doi: 10.1016/j.gpb.2017.07.002.
OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation.
Jahangiri-Tazehkand S, Wong L, Eslahchi C.

ConDens – Predict Kinase Substrates using Conservation of Local Motif Density

ConDens

:: DESCRIPTION

ConDens is a method designed to predict kinase substrate interactions using evolutionary conservation information.

::DEVELOPER

Alan Moses Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

  ConDens

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Feb 1. [Epub ahead of print]
Predicting Kinase Substrates using Conservation of Local Motif Density.
Lai AC, Nguyen Ba AN, Moses AM.

LCGserver – Exploring Conservation and Dynamics of Gene Orders

LCGserver

:: DESCRIPTION

LCGserver is a webserver for exploring evolutionary dynamics of gene orders over diverse lineages.

::DEVELOPER

CAS Key Lab of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

OMICS. 2015 Aug 10.
LCGserver: A Webserver for Exploring Evolutionary Trajectory of Gene Orders in a Large Number of Genomes.
Wang D, Yu J

NBC 1.0 – Neighborhood Breakpoint Conservation

NBC 1.0

:: DESCRIPTION

NBC (Neighborhood Breakpoint Conservation) is a method that identifies recurrent copy number variants in multiple individuals using Array Comparative Genomic Hybridization (aCGH).aCGH computes the ratio of test:reference DNA for probes located on the reference genome. NBC first uses a Bayesian changepoint algorithm to identify probes, called breakpoints, that change from low-to-high or high-to-low copy number with high probability. A binomial statistic is then applied to identify breakpoints and pairs of breakpoints that appear in a statistically significant number of individuals.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsx/WIndows
  • Java

:: DOWNLOAD

 NBC

:: MORE INFORMATION

Citation

A. Ritz, P.L. Paris, M.M. Ittmann, C. Collins, and B.J. Raphael. (2011)
Detection of Recurrent Rearrangement Breakpoints from Copy Number Data.
BMC Bioinformatics 2011, 12:114 doi:10.1186/1471-2105-12-114

ECR Browser – Interactive Browser of Genome Conservation and Evolution

ECR Browser

:: DESCRIPTION

The ECR Browser is a dynamic graphical interface that allows users to visualize and analyze Evolutionary Conserved Regions (ECRs) in genomes of sequenced species.

::DEVELOPER

Ivan Ovcharenko Research Group

:: SCREENSHOTS

ECRBrowser

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.
Ovcharenko I, Nobrega MA, Loots GG, Stubbs L.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W280-6.

SCONE 0.61 – Sequence CONservation Evaluation

SCONE 0.61

:: DESCRIPTION

SCONE (Sequence CONservation Evaluation) reports position-specific measures of conservation.

::DEVELOPER

Sunyaev Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 SCONE

:: MORE INFORMATION

Citation

Analysis of sequence conservation at nucleotide resolution.
Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S.
PLoS Comput Biol. 2007 Dec;3(12):e254. Epub 2007 Nov 14.