TinT – Screening for Nested Transpositions from Genome Assemblies or Trace data

TinT

:: DESCRIPTION

TinT (Transposition in Transposition) affords an easy, automated screening for nested transpositions from genome assemblies or trace data, assembles them in a frequency-matrix, and schematically displays their chronological activity history

::DEVELOPER

Institute of Bioinformatics WWU Muenster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Window / MacOsX
  • Java

:: DOWNLOAD

 TinT

:: MORE INFORMATION

Citation

Churakov G, Grundmann N, Kuritzin A, Brosius J, Makalowski W, Schmitz J. (2010)
A Novel Web-Based TinT Application and the Chronology of the Primate Alu Retroposon Activity.
BMC Evolutionary Biology 10:376.

findIR – Detection of Perfect Overlapping and Nested Inverted Repeats in DNA Sequences

findIR

:: DESCRIPTION

Palindrome (also known as findIR) is a MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • MatLab

:: DOWNLOAD

 Palindrome

:: MORE INFORMATION

Citation

A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences.
Sreeskandarajan S, Flowers MM, Karro JE, Liang C.
Bioinformatics. 2013 Nov 30.

B-NEM – Boolean Nested Effect Models

B-NEM

:: DESCRIPTION

B-NEM combines the use of downstream effects with the higher resolution of signalling pathway structures in Boolean Networks.

::DEVELOPER

B-NEM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 B-NEM

:: MORE INFORMATION

Citation

Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models.
Pirkl M, Hand E, Kube D, Spang R.
Bioinformatics. 2015 Nov 17. pii: btv680.

EXPANDS 2.1.2 – Expanding Ploidy and Allele-Frequency on Nested Subpopulations

EXPANDS 2.1.2

:: DESCRIPTION

EXPANDS characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux
  • R

:: DOWNLOAD

EXPANDS

:: MORE INFORMATION

Citation

Andor, N., Harness, J. V., Müller, S., Mewes, H. W. & Petritsch, C.
EXPANDS: expanding ploidy and allele frequency on nested subpopulations.
Bioinforma. Oxf. Engl. 30, 50–60 (2014).

K2N – Service to Get from Knotted to Nested RNA Structures

K2N

:: DESCRIPTION

K2N (Knotted To Nested) a service to get from knotted to nested RNA structures. This site provides access to a variety of methods for pseudoknot removal.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 K2N

:: MORE INFORMATION

Citation

Sandra Smit, Kristian Rother, Jaap Heringa, and Rob Knight.
From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.
RNA (2008) 14(3):410-416.

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