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Graemlin specifications


Unique identifier OMICS_04883
Name Graemlin
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


Unique identifier OMICS_04883
Name Graemlin
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Graemlin

Graemlin citations


The post genomic era of biological network alignment

EURASIP J Bioinform Syst Biol
PMCID: 5270500
PMID: 28194172
DOI: 10.1186/s13637-015-0022-9

[…] random walks using markov chains iteratively. alignmcl first builds a weighted alignment graph the same way as alignnemo. next, it applies mcl to this graph to identify conserved protein modules., graemlin 1.0 [] is an early multiple aligner. based on a phylogenetic tree of species whose networks are being aligned, it uses a “progressive alignment” strategy by performing successively pairwise […]


Applied Graph Mining Algorithms to Study Biomolecular Interaction Networks

Biomed Res Int
PMCID: 3996886
PMID: 24800226
DOI: 10.1155/2014/439476

[…] graphlets., regardless of if the calculation is for local or global alignments, performing efficient and accurate alignments on multiple networks continues to be challenging. nevertheless, the graemlin algorithm was the first algorithm capable of performing scalable, multiple network alignments []. graemlin starts from pairwise network alignments. it uses a seed-and-extend algorithm […]


A subgraph isomorphism algorithm and its application to biochemical data

BMC Bioinformatics
PMCID: 3633016
PMID: 23815292
DOI: 10.1186/1471-2105-14-S7-S13

[…] size of semidense patterns. however, this is not always true (see table - additional file ). sometimes, larger patterns may have fewer matches. in real data, this depends on the nature of the data., graemlin dataset this dataset contains 10 microbial networks (campylobacter jejuni, caulobacter crescentus, helicobacter pylori 26695, salmonella typhimurium lt2, synechocystis pcc6803, vibrio […]


Comparative interactomics with Funcoup 2.0

Nucleic Acids Res
PMCID: 3245127
PMID: 22110034
DOI: 10.1093/nar/gkr1062

[…] predict protein function but also because on the proteome scale it is an algorithmically and computationally very challenging problem. several tools exist, for instance networkblast (), isorankn (), graemlin () and graphcrunch (). these use different methods and heuristics to align networks on the basis of features such as sequence similarity, network topology similarity, functional similarity […]


The Human Bacterial Pathogen Protein Interaction Networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis

PLoS One
PMCID: 2918508
PMID: 20711500
DOI: 10.1371/journal.pone.0012089

[…] we applied four published algorithms for identifying conserved protein interaction modules (cpims) amongst the three human-pathogen networks and homology relationships previously identified: graemlin , match-and-split , networkblast , and graphhopper . these methods were originally designed to identify conserved modules between intra-species ppi networks. graemlin requires the user […]


Functionally guided alignment of protein interaction networks for module detection

PMCID: 2778333
PMID: 19797409
DOI: 10.1093/bioinformatics/btp569

[…] of interactions. networkblast has been used to perform three-way comparisons of yeast, worm and fly which yielded conserved modules displaying good overlap with mips (mewes et al., ) complexes. graemlin (flannick et al., ) use progressive pair-wise alignments to compare multiple networks. graemlin's probabilistic formulation of the topology-matching problem eliminates restrictions […]

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Graemlin institution(s)
Department of Computer Science, Stanford University, Stanford, CA, USA

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