GRASP 0.0.4 – Guided Reference-based Assembly of Short Peptides

GRASP 0.0.4

:: DESCRIPTION

GRASP is a gene annotation tool for metagenomic studies. GRASP assembles the fragmented short-peptides, which are called from the NGS reads, and aligns the assembled contigs to the query reference protein. GRASP achieves much higher sensitivity than BLASTP for gene annotation purpose.

::DEVELOPER

GRASP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GRASP

:: MORE INFORMATION

Citation

GRASP: Guided Reference-based Assembly of Short Peptides.
Zhong C, Yang Y, Yooseph S.
Nucleic Acids Res. 2014 Nov 20. pii: gku1210

GRASP 2 -Visualization of Macromolecular Structures and Sequences

GRASP 2

:: DESCRIPTION

GRASP (Graphical Representation and Analysis of Structural Properties) is a program used for macromolecular structure and surface visualization. It contains a large number of new features and scientific tools: Enhanced GUI; Structure alignment and domain database scanning; A gaussian surface generator and new surface coloring schemes; Sequence visualization and alignment; Completed work can be stored in project files; Among the many objects that can be stored in a project file are views of the structure; defined subsets, surfaces; Direct printing to printers at full printer resolution.

::DEVELOPER

Barry Honig’s group

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

GRASP

:: MORE INFORMATION

Citation

Petrey, D. and Honig, B. (2003)
GRASP2: Visualization, Surface Properties, and Electrosttics of Macromolecular Structures and Sequences.
Methods in Enzymology. 374: 492-509

GrASP 0.6 beta – Graphical Assessment of Sliding P-values

GrASP 0.6 beta

:: DESCRIPTION

GrASP (Graphical Assessment of Sliding P-values) is a graphical tool to display and assess p-values from sliding window tests. It can present thousands of p-values from the sliding window tests as a simple graphic that uses varying levels of user-specified color to indicate the width of the sliding windows and the varying levels of significance. It therefore allows the user to identify regions/blocks of interest from these sliding windows, based jointly on the absolute p-value of the tests from these windows and the building of haplotypes of significance in the region. GrASP is executed as an Excel macro and is written in Excel’s built-in version of Visual Basic for Applications.

::DEVELOPER

Rasika Mathias @ NHGRI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
Excel
Perl

:: DOWNLOAD

GrASP

:: MORE INFORMATION

Citation:

Mathias, R.A., Gao, P., Goldstein, J.L., Wilson, A.F., Pugh, E.W., Furbert-Harris, P., Dunston, G., Malveaux, F., Togias, A., Barnes, K.C., Beaty, T.H., Huang, S.K. 2006.
A graphical assessment of p-values from sliding window haplotype tests of association to identify asthma susceptibility loci on chromosome 11q.
BMC Genet. 14;7(1):38.