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MatAlign specifications


Unique identifier OMICS_03660
Name MatAlign
Alternative name Matrix Alignment
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein information
Input format PDB
Output data PDBID, number of residues in the given chain of protein, number of residues that are matched/ aligned/ equivalent, percent of aligned residues, alignment lenght, RMSD, alignment score, normalized alignment scoreLinux, WindowsAdvanced
Operating system Unix/Linux, Windows
Computer skills Advanced
Version 1.1
Stability Stable
C Clustering
Maintained Yes




No version available



  • person_outline Zeyar Aung <>

Publication for Matrix Alignment

MatAlign citations


Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans

PMCID: 3337475
PMID: 22540038
DOI: 10.1534/g3.111.001081

[…] redundancy of the whole genome motif profile set, we used the average log likelihood ratio (allr) statistic () to determine the similarity between motif profiles. allr statistics are implemented in matalign-v4a (wang and stormo; similarity of two motif profiles is determined by the allr scores of each pair of motif profiles and the length of the aligned part […]


A simple and fast heuristic for protein structure comparison

PMCID: 2335283
PMID: 18366735
DOI: 10.1186/1471-2105-9-161

[…] of queries over the nh3d database [] to evaluate the capability of a nearest neighbor classification to detect similarity at cath's architecture level. comparisons are then made against dalilite and matalign., for this experiment we use again skolnick's dataset from [,], which includes a "cluster" label for every protein corresponding to different families in scop database []. we perform […]

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MatAlign institution(s)
Institute for Infocomm Research, Singapore; School of Computing, National University of Singapore, Singapore

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