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Panaconda: Application of pan-synteny graph models to genome content analysis

https://doi.org/10.1101/215988
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-642-04241-6_19openalex-snapshot
Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes
inferredcites →https://doi.org/10.1016/j.mib.2014.11.016openalex-snapshot
Ten years of pan-genome analyses
inferredcites →https://doi.org/10.1016/s0923-2508(00)90130-xopenalex-snapshot
Genetic organisation of the lipopolysaccharide O-antigen biosynthesis region of 16M ( )
inferredcites →https://doi.org/10.1038/srep44420openalex-snapshot
Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts
inferredcites →https://doi.org/10.1093/bioinformatics/18.3.452openalex-snapshot
Multiple sequence alignment using partial order graphs
inferredcites →https://doi.org/10.1093/bioinformatics/btq465openalex-snapshot
DRIMM-Synteny: decomposing genomes into evolutionary conserved segments
inferredcites →https://doi.org/10.1093/bioinformatics/btu259openalex-snapshot
Evaluating synteny for improved comparative studies
inferredcites →https://doi.org/10.1093/bioinformatics/btu756openalex-snapshot
SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips
inferredcites →https://doi.org/10.1093/bioinformatics/btv421openalex-snapshot
Roary: rapid large-scale prokaryote pan genome analysis
inferredcites →https://doi.org/10.1093/nar/gkg500openalex-snapshot
Multiple sequence alignment with the Clustal series of programs
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkp698openalex-snapshot
FIGfams: yet another set of protein families
inferredcites →https://doi.org/10.1093/nar/gkt1274openalex-snapshot
RefSeq microbial genomes database: new representation and annotation strategy
inferredcites →https://doi.org/10.1093/nar/gkw1017openalex-snapshot
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
inferredcites →https://doi.org/10.1101/gr.082784.108openalex-snapshot
Breakpoint graphs and ancestral genome reconstructions
inferredcites →https://doi.org/10.1101/gr.174920.114openalex-snapshot
Alignathon: a competitive assessment of whole-genome alignment methods
inferredcites →https://doi.org/10.1101/gr.2289704openalex-snapshot
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
inferredcites →https://doi.org/10.1101/gr.2395204openalex-snapshot
De Novo Repeat Classification and Fragment Assembly
inferredcites →https://doi.org/10.1101/gr.2657504openalex-snapshot
A novel method for multiple alignment of sequences with repeated and shuffled elements
inferredcites →https://doi.org/10.1109/pacificvis.2011.5742389openalex-snapshot
Multilevel agglomerative edge bundling for visualizing large graphs
inferredcites →https://doi.org/10.1109/tnb.2016.2554150openalex-snapshot
Computational Synteny Block: A Framework to Identify Evolutionary Events
inferredcites →https://doi.org/10.1128/jb.01202-08openalex-snapshot
A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera
inferredcites →https://doi.org/10.1128/jb.01767-08openalex-snapshot
Analysis of TenBrucellaGenomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle
inferredcites →https://doi.org/10.1128/jb.185.20.6130-6136.2003openalex-snapshot
Molecular Characterization of Brucella abortus Chromosome II Recombination
inferredcites →https://doi.org/10.1128/mbio.00246-12openalex-snapshot
Comparative Genomics of Early-DivergingBrucellaStrains Reveals a Novel Lipopolysaccharide Biosynthesis Pathway
inferredcites →https://doi.org/10.1128/mbio.00388-12openalex-snapshot
Comparative Genomics of Early-Diverging Brucella Strains Reveals a Novel Lipopolysaccharide Biosynthesis Pathway
inferredcites →https://doi.org/10.1186/1471-2164-15-s6-s6openalex-snapshot
What is the difference between the breakpoint graph and the de Bruijn graph?
inferredcites →https://doi.org/10.1371/journal.pone.0002760openalex-snapshot
Brucellosis Vaccines: Assessment of Brucella melitensis Lipopolysaccharide Rough Mutants Defective in Core and O-Polysaccharide Synthesis and Export
inferredcites →https://doi.org/10.1371/journal.pone.0098679openalex-snapshot
ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software
inferredcites →https://doi.org/10.1609/icwsm.v3i1.13937openalex-snapshot
Gephi: An Open Source Software for Exploring and Manipulating Networks
inferredcites →https://doi.org/10.25080/tcwv9851openalex-snapshot
Exploring Network Structure, Dynamics, and Function using NetworkX
inferredcites →https://doi.org/10.3389/fcimb.2016.00116openalex-snapshot
A Brucella spp. Isolate from a Pac-Man Frog (Ceratophrys ornata) Reveals Characteristics Departing from Classical Brucellae
inferredcites →https://doi.org/10.3389/fmicb.2016.00118openalex-snapshot
PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-3-030-38281-0_4openalex-snapshot
A Review of Pangenome Tools and Recent Studies
inferred← citeshttps://doi.org/10.1007/s41745-021-00255-zopenalex-snapshot
Methods and Developments in Graphical Pangenomics
inferred← citeshttps://doi.org/10.1063/5.0152644openalex-snapshot
Method of genomes comparative analysis using graph DBMS
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty614openalex-snapshot
Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations
inferred← citeshttps://doi.org/10.1128/mmbr.00403-25openalex-snapshot
The grammar of the pangenome: terms, concepts, methods, and emerging patterns—a general framework for comparative genomics and genome biology
inferred← citeshttps://doi.org/10.1177/1177932218825127openalex-snapshot
Combining Strengths for Multi-genome Visual Analytics Comparison
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