Supplementary Data for "Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants"
Dörr D, Rubert D (2019)
Bielefeld University.
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Data for: Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants
This dataset contains the main computed data used in that work. Find below a list of packages and a summary of their content. Next, each package is described in detail.
coffee.gbk
grape.gbk
lettuce.gbk
sunflower.gbk
Customized/filtered genbank files of species. #### atoms.tar.bz2 ag100_ai30_al13_m100.atoms : Computed atoms, that is, a list of genes and their families. #### syntenic_blocks.tar.bz2 ag100_ai30_al13_m100.cog : Sequence of genes in each chromosome (Gecko3-DCJ input genomes format).
rgrape_q3_dcj_dcjBorderline8_dcjPenality0.25_dcjUseHeuristics_dT0_0_0_2__1_0_1_3 ... .gckz : Sequence of genes in each chromosome with computed syntenic blocks and local DCJ similarity (Gecko3-DCJ session format).
rgrape_q3_dcj_dcjBorderline8_dcjPenality0.25_dcjUseHeuristics_dT0_0_0_2__1_0_1_3 ... .clusters : Syntenic blocks found by Gecko3-DCJ (Gecko3-DCJ clusters export format).
#### syntenic_blocks_refined.tar.bz2 refoverlap_refsim.genesmap : Map of new refined gene families. Each line contains two values, the first one is the new (refined) family number and the second one is the old family number. refoverlap_refsim_refined.cog : Sequence of genes in each chromosome (Gecko3-DCJ input genomes format). refoverlap_refsim_refined.gckz : Sequence of genes in each chromosome with computed syntenic blocks and local DCJ similarity (Gecko3-DCJ session format). refoverlap_refsim_refined.clusters : Syntenic blocks found by Gecko3-DCJ (Gecko3-DCJ clusters export format). refoverlap_refsim_refined.acs : Syntenic blocks as ACSs (ANGES format). refoverlap_refsim_refined.clustersmap : Map of syntenic blocks IDs. Each line maps an ID in the refoverlap_refsim_refined.acs file to an ID in the refoverlap_refsim_refined.clusters file. #### ancestor.tar.bz2 eudicots_ACS_C1P_HEUR : ACSs selected to compose the reconstructed ancestor. eudicots_PQTREE_HEUR : PQ-tree representing the reconstructed ancestor.
This dataset contains the main computed data used in that work. Find below a list of packages and a summary of their content. Next, each package is described in detail.
- extant_eudicot_genomes.tar.bz2 : Genome sequence files.
- atoms.tar.bz2 : Computed atoms.
- syntenic_blocks.tar.bz2 : Files related to syntenic blocks found.
- syntenic_blocks_refined.tar.bz2 : Files related to syntenic blocks found after the family refinement process.
- ancestor.tar.bz2 : Files related to the reconstructed ancestor.
coffee.gbk
grape.gbk
lettuce.gbk
sunflower.gbk
Customized/filtered genbank files of species. #### atoms.tar.bz2 ag100_ai30_al13_m100.atoms : Computed atoms, that is, a list of genes and their families. #### syntenic_blocks.tar.bz2 ag100_ai30_al13_m100.cog : Sequence of genes in each chromosome (Gecko3-DCJ input genomes format).
rgrape_q3_dcj_dcjBorderline8_dcjPenality0.25_dcjUseHeuristics_dT0_0_0_2__1_0_1_3 ... .gckz : Sequence of genes in each chromosome with computed syntenic blocks and local DCJ similarity (Gecko3-DCJ session format).
rgrape_q3_dcj_dcjBorderline8_dcjPenality0.25_dcjUseHeuristics_dT0_0_0_2__1_0_1_3 ... .clusters : Syntenic blocks found by Gecko3-DCJ (Gecko3-DCJ clusters export format).
#### syntenic_blocks_refined.tar.bz2 refoverlap_refsim.genesmap : Map of new refined gene families. Each line contains two values, the first one is the new (refined) family number and the second one is the old family number. refoverlap_refsim_refined.cog : Sequence of genes in each chromosome (Gecko3-DCJ input genomes format). refoverlap_refsim_refined.gckz : Sequence of genes in each chromosome with computed syntenic blocks and local DCJ similarity (Gecko3-DCJ session format). refoverlap_refsim_refined.clusters : Syntenic blocks found by Gecko3-DCJ (Gecko3-DCJ clusters export format). refoverlap_refsim_refined.acs : Syntenic blocks as ACSs (ANGES format). refoverlap_refsim_refined.clustersmap : Map of syntenic blocks IDs. Each line maps an ID in the refoverlap_refsim_refined.acs file to an ID in the refoverlap_refsim_refined.clusters file. #### ancestor.tar.bz2 eudicots_ACS_C1P_HEUR : ACSs selected to compose the reconstructed ancestor. eudicots_PQTREE_HEUR : PQ-tree representing the reconstructed ancestor.
Stichworte
eudicot ancestor;
plant evolution;
ancestral reconstruction;
comparative genomics;
computational biology
Erscheinungsjahr
2019
Copyright und Lizenzen
Page URI
https://pub.uni-bielefeld.de/record/2936848
Zitieren
Dörr D, Rubert D. Supplementary Data for "Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants". Bielefeld University; 2019.
Dörr, D., & Rubert, D. (2019). Supplementary Data for "Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants". Bielefeld University. https://doi.org/10.4119/unibi/2936848
Dörr, Daniel, and Rubert, Diego. 2019. Supplementary Data for "Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants". Bielefeld University.
Dörr, D., and Rubert, D. (2019). Supplementary Data for "Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants". Bielefeld University.
Dörr, D., & Rubert, D., 2019. Supplementary Data for "Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants", Bielefeld University.
D. Dörr and D. Rubert, Supplementary Data for "Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants", Bielefeld University, 2019.
Dörr, D., Rubert, D.: Supplementary Data for "Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants". Bielefeld University (2019).
Dörr, Daniel, and Rubert, Diego. Supplementary Data for "Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants". Bielefeld University, 2019.
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ancestor.tar.bz2
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2019-08-13T06:31:06Z
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atoms.tar.bz2
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2019-08-13T06:31:12Z
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syntenic_blocks_refined.tar.bz2
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2019-08-13T06:31:20Z
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syntenic_blocks.tar.bz2
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2019-08-13T06:31:22Z
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extant_eudicot_genomes.tar.bz2
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2019-09-12T10:03:10Z
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ANGORA.zip
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