Valmei lab

Plant-FUNCO



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DOI

  1. QUERY-TARGET.next.axt Comparative Genomics: .net.axt includes a set of files describing the alignments derived from whole genome alignment pipeline. A total of 6 .net.axt files are available taking into account all pairwise query-target combinations between the three model species in PlantFUNCO.
  2. QUERY-TARGET_LECIFscore.bedgraph Functional Genomics: *_LECIFscore.bedgraph includes a set of files reporting functional genomics conservation scores derived from LECIF algorithm. A total of 6 files are available taking into account all pairwise query-target combinations between the three model species in PlantFUNCO. At = Arabidopsis thaliana, Os = Oryza sativa, Zm = Zea mays.
  3. QUERY_PhyloP_merged.bedgraph Comparative Genomics: *_PhyloP_merged.bedgraph includes a set of files reporting merged evolutionary conservation at individual alignment sites from PlantRegMap. A total of 3 files are available taking into account each of the three model species in PlantFUNCO. Ath = Arabidopsis thaliana, Osj = Oryza sativa, Zma = Zea mays.
  4. CNE_QUERY_TARGET_45_50.bed Comparative Genomics: CNE_QUERY_TARGET_45_50.bed includes a set of files reporting pairwise conserved non-coding elements (CNEs) from whole genome alignment pipeline + CNEr with 90% identity threshold. A total of 6 files are available taking into account all pairwise query-target combinations between the three model species in PlantFUNCO.
  5. *_CNEdb.sqlite Comparative Genomics: *_CNEdb.sqlite summarizes all previous CNEs information into a single and database-friendly file. A total of 3 files are available taking into account all bidirectional query-target combinations between the three model species in PlantFUNCO.
  6. hihmm.model1.K15.QUERY.*.bed Functional Genomics: hihmm.model1.K15.QUERY.*.bed includes a set of files reporting inter-species chromatin states from hiHMM algorithm. Further details on chromatin states annotation and interpretation can be found in the slider third image of Home tab or in the manuscript. A total of 3 files are available taking into account each of the three model species in PlantFUNCO.