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AutoGRAPH specifications

Information


Unique identifier OMICS_11722
Name AutoGRAPH
Interface Web user interface
Restrictions to use None
Input data Preinserted datasets, Personal datasets
Output data The program output consists of: (i) a figure showing gene order relationships by means of connecting lines within each CS and conserved segments ordered (CSO), across two to three species, and identifying the evolutionary breakpoint regions delimiting CS and/or CSO; (ii) two modes, making it possible to construct comparative maps with or without one-to-zero relationship anchors, to switch the orientation of each map and to scale images by a factor of 0.5 to 2; (iii) a table listing all CS, CSO and breakpoints, with their size, number of genes, chromosome coordinates and gene density.
Programming languages PHP
Database management system MySQL
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Publication for AutoGRAPH

AutoGRAPH in pipeline

2017
PMCID: 5240624
PMID: 28094805
DOI: 10.1038/srep40728

[…] orthomcl analysis (linking a gene in a mapped contig with the physical position of its putative ortholog in a. lyrata). comparisons for each linkage group are shown in . images were generated using autograph. we also evaluated the microsynteny between b. vulgaris and a. lyrata using simplesynteny for several b. vulgaris contigs (). b. vulgaris contigs with sequence homology to a. lyrata […]


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AutoGRAPH in publications

 (4)
PMCID: 5240624
PMID: 28094805
DOI: 10.1038/srep40728

[…] orthomcl analysis (linking a gene in a mapped contig with the physical position of its putative ortholog in a. lyrata). comparisons for each linkage group are shown in . images were generated using autograph. we also evaluated the microsynteny between b. vulgaris and a. lyrata using simplesynteny for several b. vulgaris contigs (). b. vulgaris contigs with sequence homology to a. lyrata […]

PMCID: 4609151
PMID: 26475137
DOI: 10.1186/s12864-015-2030-2

[…] affolds []., as the consensus map by huang et al. [] and the rh map by tiwari et al. [] have dart markers with the same nomenclature, these maps were directly compared with the present rh maps, using autograph (http://autograph.genouest.org; []). however, to identify the common markers in luo et al. [], the available dart sequences were used to blast compare against the sequences containing snp ma […]

PMCID: 2689173
PMID: 19416516
DOI: 10.1186/1471-2148-9-89

[…] genes between both human/dog and human/mouse, which we downloaded from biomart [] in ensembl []. 0.5% of total alignment blocks were discarded because they were non-syntenic. we also used autograph [], a web based synteny visualization tool, to inspect synteny structures., when comparing two lineages we chose members of our repeat dataset using the following conditions: 1) each repeat […]

PMCID: 2644713
PMID: 19193219
DOI: 10.1186/1471-2164-10-62

[…] the set of 412 protein-coding genes not annotated on the dog genome assembly with a 1:1:1:1:0 human:chimp:mouse:rat:dog match was then extracted from the mysql database., we used the program autograph [] to construct pairwise synteny maps between reference genomes and tested genome. autograph has been designed to construct synteny maps using genomic coordinates of ortholog pairs. […]


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AutoGRAPH institution(s)
CNRS UMR6061 Génétique et Développement, Université de Rennes1 IFR140, Rennes, France

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