STRAP 20200621 – STRucture-based Sequence Alignment Program

STRAP 20200621

:: DESCRIPTION

Strap (STRucture-based Sequence Alignment Program) aligns proteins by sequence and 3D-structure.Strap supports the simultaneous analysis of hundreds of proteins and integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence and residue annotation.

::DEVELOPER

Christoph Gille

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

STRAP

:: MORE INFORMATION

Citation

HotSwap for bioinformatics: a STRAP tutorial.
Gille C, Robinson PN.
BMC Bioinformatics. 2006 Feb 9;7:64.

HMMSUM – Structure-based Substitution Matrices

HMMSUM

:: DESCRIPTION

HMMSUM (HMMSTR-based SUbstitution matrices) is a new model for structural context-based amino acid substitution probabilities consisting of a set of 281 matrices, each for a different sequence-structure context. HMMSUM does not require the structure of the protein to be known. Instead, predictions of local structure are made using HMMSTR, a hidden Markov model for local structure. Alignments using the HMMSUM matrices compare favorably to alignments carried out using the BLOSUM50 matrix when validated against curated remote homolog alignments from BAliBASE. HMMSUM has been implemented using local Dynamic Programming and with the Bayesian Adaptive alignment method. The download package contains the essential programs from HMMSTR (see above) and the HMMSTR model itself, alng with Smith-Waterman local dynamic programming and Bayesian Adaptive alignment programs, modified to use the HMMSUM matrices.

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

HMMSUM

:: MORE INFORMATION

Citaiton

Huang, Y-M, & Bystroff, C. (2006)
Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions.
Bioinformatics 22(4):413-422