SAS-Pro 201106 – Sequential and Non-sequential Structure Alignment of Proteins

SAS-Pro 201106

:: DESCRIPTION

The SAS-Pro software provides an optimal structural alignment between any given pair of proteins. It is based on an algorithm for Simultaneous Alignment and structure Superposition of PROteins (SAS-Pro). SAS-Pro provides both sequential and non-sequential protein alignments.

::DEVELOPER

Nikolaos V. Sahinidis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MATLAB
  • gfortran compiler 4.4.1 or newer version

:: DOWNLOAD

 SAS-Pro

:: MORE INFORMATION

Citation

S. B. Shah and N. V. Sahinidis,
SAS-Pro: Simultaneous Residue Assignment and Structure Superposition for Protein Structure Alignment,
PLoS ONE 7(5): e37493.

SNAP 20080926 / FlexSnap 20091128 – Non-sequential Pair-wise Structural Alignment

SNAP 20080926 / FlexSnap 20091128

:: DESCRIPTION

SNAP finds non-sequential 3D protein structure alignments. It was initially called STSA

FlexSnap allows the ability to find both flexible and non-sequential allignments.

::DEVELOPER

Mohammed J. Zaki

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SNAP , FlexSnap

:: MORE INFORMATION

Citation

Saeed Salem, Mohammed J. Zaki and Chris Bystroff,
Iterative Non-Sequential Protein Structural Alignment.
Journal of Bioinformatics and Computational Biology, 7(3):571-596. Jun 2009

Algorithms Mol Biol. 2010 Jan 4;5:12. doi: 10.1186/1748-7188-5-12.
FlexSnap: flexible non-sequential protein structure alignment.
Salem S1, Zaki MJ, Bystroff C.

SplicePie – Pipeline to Analyze Non-sequential and Multi-step Splicing

SplicePie

:: DESCRIPTION

SplicePie contains three major analysis steps: analyzing the order of splicing per sample, looking for recursive splicing events per sample and summarizing predicted recursive splicing events for all analyzed sample (it is recommended to use more samples for higher reliability). The first two steps are performed individually on each sample and the last step looks at the overlap in all samples. However, the analysis can be run on one sample as well.

::DEVELOPER

SplicePie team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SplicePie

:: MORE INFORMATION

Citation

SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing.
Pulyakhina I, Gazzoli I, Hoen PB, Verwey N, den Dunnen J, Aartsma-Rus A, Laros J.
Nucleic Acids Res. 2015 Mar 23. pii: gkv242.