jEcho 1.0 – An Evolved Weight Vector to CHaracterize the protein’s post-translational Modification mOtifs

jEcho 1.0

:: DESCRIPTION

jEcho is an Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.

::DEVELOPER

Fengfeng Zhou

:: SCREENSHOTS

jEcho

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • Java

:: DOWNLOAD

 jEcho

:: MORE INFORMATION

Citation

Interdiscip Sci. 2015 Jun;7(2):194-9. doi: 10.1007/s12539-015-0260-2. Epub 2015 Aug 6.
jEcho: an Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.
Zhao M, Zhang Z, Mai G, Luo Y, Zhou F.

LocalDiff 201309 – Characterize Non-stationary Patterns of Isolation by Distance

LocalDiff 201309

:: DESCRIPTION

LocalDiff provides Bayesian measures of Local Genetic Differentiation to characterize non-stationary patterns of isolation by distance.

::DEVELOPER

Nicolas Duforet-Frebourg and Michael Blum

:: SCREENSHOTS

LocalDiff

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 LocalDiff

:: MORE INFORMATION

Citation

Non-stationary patterns of isolation-by-distance: inferring measures of genetic Friction.
Nicolas Duforet-Frebourg, Michael G. B. Blum.
arXiv:1209.5242

HELANAL-Plus – Characterize the Geometries of Helices present in Proteins

HELANAL-Plus

:: DESCRIPTION

HELANAL-Plus is a program to characterize overall geometry of helices from its C-alpha atom coordinates. This program can be very useful in analysis of protein secondary structure, modeling of membrane proteins, analysis of molecular dynamics runs of helices or alpha helical proteins, designed peptides containing helical motifs, etc.

::DEVELOPER

Prof. Manju Bansal Lab, MBU, IISc, Bangalore, India.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 HELANAL-Plus

:: MORE INFORMATION

Citation

Kumar, P. & Bansal, M. (2012).
HELANAL-Plus: a web server for analysis of helix geometry in protein structures.
J Biomol Struct Dyn. 30: 773-783

RetroMap 0.021 – Characterize LTR Retroelements on a Genome Scale

RetroMap 0.021

:: DESCRIPTION

RetroMap is an application designed to help characterize LTR retroelements on a genome scale in a visually interactive manner. This is NOT a particularly great for comprehensive identification of elements found in highly nested contexts. Only the most internal element of those which are nested is likely to be identified as a complete element. The other elements will be treated as solo LTRs and internal regions depending on how you have set up your element searches. However, it is still a handy way to get a quick visual overview of the situation and create pretty figures.

::DEVELOPER

Brooke D. Peterson-Burch. 

:: SCREENSHOTS

RetroMap

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • Java

:: DOWNLOAD

 RetroMap

:: MORE INFORMATION

Citation

Genome Biol. 2004;5(10):R78. Epub 2004 Sep 29.
Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae.
Peterson-Burch BD, Nettleton D, Voytas DF.