Genome Maps specifications

Information


Unique identifier OMICS_06400
Name Genome Maps
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Animals
    • Bombyx mori
    • Bos taurus
    • Caenorhabditis elegans
    • Danio rerio
    • Drosophila melanogaster
    • Homo sapiens
    • Mus musculus
    • Rattus norvegicus
  • Fungi
    • Aspergillus fumigatus
    • Saccharomyces cerevisiae
    • Schizosaccharomyces pombe
  • Plants
    • Arabidopsis thaliana
    • Glycine max
    • Hordeum vulgare
    • Populus trichocarpa
    • Vitis vinifera
    • Zea mays
  • Protists
    • Dictyostelium discoideum
    • Giardia lamblia
    • Leishmania major
    • Plasmodium falciparum

Documentation


Maintainers


  • person_outline Joaquín Dopazo <>
  • person_outline Ignacio Medina <>
  • person_outline Francisco Salavert <>

Additional information


https://github.com/opencb/genome-maps/wiki

Genome Maps article

Genome Maps citations

 (4)
2018
PMCID: 5833319

[…] of as to ts (at skew = [a – t]/[a + t]) and gs to cs (gc skew = [g – c]/[g + c]) (perna and kocher 1995). overlapping regions and intergenic spacers between genes were counted manually. circular genome maps were generated by organellargenomedraw (lohse et al. 2013) and revised by hand. the sequence data were deposited in genbank under accession mg460483., to reconstruct the phylogenetic […]

2017
PMCID: 5468394

[…] with five iterations (with options -inclusion_ethresh 1e-5 and -evalue 1e-5). trnascan-se 1.3.1 (option: -b for bacterial trnas) was used to identify trna genes (lowe and eddy, 1997). circular genome maps were generated using cgview (stothard and wishart, 2005) and dot-plots by an in-house script. sequences were aligned using mafft v7.220 (katoh and standley, 2016) with default parameters. […]

2016
PMCID: 5073276

[…] usa). de novo assemblies were individually produced and merged using geneious version 9.1.3 (11) and clc genomics workbench version 9.0 (https://www.qiagenbioinformatics.com). pacbio reads and whole-genome maps were used for scaffolding and genome closure (12). automated annotation for strain 063228 was performed using the rast server (http://rast.nmpdr.org), while the ncbi prokaryote genome […]

2016
PMCID: 4762882

[…] 150 kbp. data from each sample were assembled using an in-house developed de novo assembler based on overlap-layout-consensus paradigm141516. the n50 length is the length for which the collection of genome maps of that length or greater cover >50% of the total genome length. the genome maps in this study had a n50 of >0.9 mbp, overlapping close to 90% of the genome reference consortium […]

Genome Maps institution(s)
Department of Computational Genomics, Centro de Investigacion Principe Felipe (CIPF), Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain; Genometra S.L., Valencia, Spain; Functional Genomics Node (INB) at CIPF, Valencia, Spain

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