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MAPGAPS specifications


Unique identifier OMICS_12075
Alternative name Multiply-Aligned Profiles for Global Alignment of Protein Sequences
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.0.1
Stability Stable
Maintained Yes


No version available



  • person_outline Andrew F. Neuwald

Publication for Multiply-Aligned Profiles for Global Alignment of Protein Sequences

MAPGAPS citations


Inferring joint sequence structural determinants of protein functional specificity

PMCID: 5770160
PMID: 29336305
DOI: 10.7554/eLife.29880.030

[…] MAPGAPS () creates an MSA by: (1) Taking as input either a small but ideally very accurate MSA, each sequence of which represents a distinct subgroup within a protein superfamily, or, alternatively, a […]


Inference of Functionally Relevant N acetyltransferase Residues Based on Statistical Correlations

PLoS Comput Biol
PMCID: 5225019
PMID: 28002465
DOI: 10.1371/journal.pcbi.1005294

[…] those regions that are conserved across each subtree’s sequence set are aligned—as is illustrated schematically in . The hiHMM defined by this process can be used to search the protein database using MAPGAPS []. […]


Hydrophobic Core Variations Provide a Structural Framework for Tyrosine Kinase Evolution and Functional Specialization

PLoS Genet
PMCID: 4771162
PMID: 26925779
DOI: 10.1371/journal.pgen.1005885

[…] Crystal structural analysis was carried out on 4100 protein kinase chains obtained from PDB. Sequences corresponding to the kinase domain were aligned using MAPGAPS to map structurally equivalent positions. The aligned positions were manually evaluated for accuracy and pair-wise interaction energy between residues was calculated using AMBER force field[]. […]


Identification and classification of small molecule kinases: insights into substrate recognition and specificity

BMC Evol Biol
PMCID: 4702295
PMID: 26738562
DOI: 10.1186/s12862-015-0576-x
call_split See protocol

[…] s ensured correct placement of intervening regions despite the absence of significant sequence similarity. The proteins within each group were aligned against that group’s representative PDB sequence.MAPGAPS [], a program to align sequences to a hierarchical set of profiles, was used to generate the final core domain alignment. The input to MAPGAPS is a set of alignment profiles, a consensus seque […]


Co Conserved MAPK Features Couple D Domain Docking Groove to Distal Allosteric Sites via the C Terminal Flanking Tail

PLoS One
PMCID: 4370755
PMID: 25799139
DOI: 10.1371/journal.pone.0119636

[…] EPK sequences from major taxonomic groups and families were aligned using the MAPGAPS program [] using curated profiles of major EPK groups and families [,,]. The C- tail sequence profile was curated using Fammer tool [] and formatted for CHAIN analysis using biocma (https://gi […]


Prediction and Prioritization of Rare Oncogenic Mutations in the Cancer Kinome Using Novel Features and Multiple Classifiers

PLoS Comput Biol
PMCID: 3990476
PMID: 24743239
DOI: 10.1371/journal.pcbi.1003545

[…] frequency of the wild-type or consensus-type residue in the alignment column. The calculations are performed on large multiple-sequence alignments using sequences from UniRef90 and aligned using the MAPGAPS program and HMMer 3.0 . […]


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MAPGAPS institution(s)
Department of Biochemistry & Molecular Biology and The Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, MD, USA
MAPGAPS funding source(s)
The NIH Division of General Medicine Grant GM078541

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