Genome Maps pipeline

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


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

Documentation


Maintainers


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

Additional information


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

Publication for Genome Maps

Genome Maps IN pipelines

 (8)
2018
PMCID: 5833319
PMID: 29718483
DOI: 10.1093/jisesa/iey012

[…] 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 […]

2018
PMCID: 5855824
PMID: 29463014
DOI: 10.3390/ijms19020602

[…] were annotated using dogma [45] and blast. the newly constructed chloroplast genomes were deposited in the ddbj database under the accession numbers lc361349-51. finally, the circular chloroplast genome maps were drawn using ogdraw [46]., the whole chloroplast genome sequences of a. nipponica (strain jo23: ap009369), a. stelleri (ky126841) [23], a. alpina (hf934132) [25], and d. nemorosa […]

2017
PMCID: 5389983
PMID: 28450852
DOI: 10.3389/fmicb.2017.00573

[…] cluster orthologous group (cog) and its pfam domain was performed with the ncbi's conserved domain database using an expected value threshold of 0.001 (marchler-bauer et al., 2014). the circular genome maps of the draft genome sequences of x. arboricola strains cita 14 and cita 124, representing the cog categories of the genes, were constructed using cgview (stothard and wishart, 2005). […]

2016
PMCID: 4762882
PMID: 26892726
DOI: 10.1038/ncomms10536

[…] 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 […]

2016
PMCID: 4762882
PMID: 26892726
DOI: 10.1038/ncomms10536

[…] 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 human genome (grch37; methods; supplementary fig. 2; supplementary table 1)., to assess […]

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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