cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17608/k6.auckland.14464929.v1
title: Brown snake and Tiger snake rDNA unit size files

description: Raw read files contain raw nanopore reads in FASTA format used to determine rDNA unit size for the Brown snake and Tiger snake (kindly provided by Dr Richard Edwards of The University of New South Wales, Sydney, Australia).<br>Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in FASTA format for members of the Squamata lineage (Brown snake, Tiger snake).<br>Con_indiv_units files contain individual rDNA unit sequences extracted from nanopore reads used to generate the consensus sequence in FASTA format for members of the Squamata lineage (Brown snake, Tiger snake)<br><br>Consensus_alignment files contains the alignement output in .geneious format.<br>Annotated_Consensus files contains the annotated consensus sequences in .geneious format.<br><br>align_Tigersnake/Brownsnake_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (Genbank accession X02995).<br><br>Average rDNA unit size was generated for each species using the included excel spreadsheets.<br>
DOI: 10.17608/k6.auckland.14464929
title: Brown snake and Tiger snake rDNA unit size files

description: Raw read files contain raw nanopore reads in FASTA format used to determine rDNA unit size for the Brown snake and Tiger snake (kindly provided by Dr Richard Edwards of The University of New South Wales, Sydney, Australia).<br>Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in FASTA format for members of the Squamata lineage (Brown snake, Tiger snake).<br>Con_indiv_units files contain individual rDNA unit sequences extracted from nanopore reads used to generate the consensus sequence in FASTA format for members of the Squamata lineage (Brown snake, Tiger snake)<br><br>Consensus_alignment files contains the alignement output in .geneious format.<br>Annotated_Consensus files contains the annotated consensus sequences in .geneious format.<br><br>align_Tigersnake/Brownsnake_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (Genbank accession X02995).<br><br>Average rDNA unit size was generated for each species using the included excel spreadsheets.<br>
DOI: 10.17608/k6.auckland.14464938
title: Golden-fronted woodpecker rDNA unit size files

description: GFW_rDNA_Raw_reads file contains raw nanopore reads extracted from a nanopore dataset readsf or the Golden-fronted Woodpecker (NCBI accession PRJNA598863) in FASTA format used to determine rDNA unit size.<br>GFW_con_reads file contains raw nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in FASTA format for a member of the Aves lineage (Golden-fronted Woodpecker).<br>GFW_con_indiv_units file contains individual rDNA unit sequences extracted from nanopore reads used to generate the consensus sequence in FASTA format for a member of the Aves lineage (Golden-fronted Woodpecker).<br><br>Golden-fronted Woodpecker_consensus_alignment file contains the alignement output.<br><br>annotated_GFW_consensus file contains the annotated rDNA consensus sequence.<br><br>align_GFW_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (Genbank accession KT445934).<br><br>Average rDNA unit size was generated using the included excel spreadsheet.<br>
DOI: 10.17608/k6.auckland.14464938.v1
title: Golden-fronted woodpecker rDNA unit size files

description: GFW_rDNA_Raw_reads file contains raw nanopore reads extracted from a nanopore dataset readsf or the Golden-fronted Woodpecker (NCBI accession PRJNA598863) in FASTA format used to determine rDNA unit size.<br>GFW_con_reads file contains raw nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in FASTA format for a member of the Aves lineage (Golden-fronted Woodpecker).<br>GFW_con_indiv_units file contains individual rDNA unit sequences extracted from nanopore reads used to generate the consensus sequence in FASTA format for a member of the Aves lineage (Golden-fronted Woodpecker).<br><br>Golden-fronted Woodpecker_consensus_alignment file contains the alignement output.<br><br>annotated_GFW_consensus file contains the annotated rDNA consensus sequence.<br><br>align_GFW_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (Genbank accession KT445934).<br><br>Average rDNA unit size was generated using the included excel spreadsheet.<br>
DOI: 10.17608/k6.auckland.14465049
title: Tuatara rDNA unit size files

description: reads_analysed file contains raw nanopore reads extracted from a nanopore dataset readsf or the Tuatara (NCBI accession PRJNA445603) in FASTA format used to determine rDNA unit size.<br>Con_reads files contain nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in FASTA format for the sole extant rhynchocephalia species (Tuatara).<br>Con_indiv_units files contain individual rDNA unit sequences extracted from nanopore reads used to generate the consensus sequence in FASTA format for the sole extant rhynchocephalia species (Tuatara).<br>Consensus_alignment files contains the alignement output in .geneious format.<br>Annotated_Consensus files contains the annotated consensus sequences in .geneious format.<br><br>align_Tuatara_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (Genbank accession X02995).<br>.<br>Average rDNA unit size was generated using the included excel spreadsheet.<br>
DOI: 10.17608/k6.auckland.14465049.v1
title: Tuatara rDNA unit size files

description: reads_analysed file contains raw nanopore reads extracted from a nanopore dataset readsf or the Tuatara (NCBI accession PRJNA445603) in FASTA format used to determine rDNA unit size.<br>Con_reads files contain nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in FASTA format for the sole extant rhynchocephalia species (Tuatara).<br>Con_indiv_units files contain individual rDNA unit sequences extracted from nanopore reads used to generate the consensus sequence in FASTA format for the sole extant rhynchocephalia species (Tuatara).<br>Consensus_alignment files contains the alignement output in .geneious format.<br>Annotated_Consensus files contains the annotated consensus sequences in .geneious format.<br><br>align_Tuatara_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (Genbank accession X02995).<br>.<br>Average rDNA unit size was generated using the included excel spreadsheet.<br>
DOI: 10.17608/k6.auckland.14465100.v1
title: Tasmanian Devil rDNA unit size files

description: analysed_reads file contains raw nanopore reads extracted from a nanopore dataset readsf or the Tasmanian devil (NCBI accession PRJEB34649) in FASTA format used to determine rDNA unit size..<br>Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in FASTA format.<br>Con_indiv_units files contain individual rDNA unit sequences extracted from nanopore reads used to generate the long and short consensus sequence in FASTA format.<br>Consensus_alignment files contains the alignement output in .geneious format.<br>Annotated_Consensus files contains the two annotated consensus sequences in .geneious format.<br>align_Tasmanian_Devil_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (NCBI accession GL000220; see Agrawal & Ganley, 2018).<br>Average rDNA unit size was generated using the included excel spreadsheet.<br>
DOI: 10.17608/k6.auckland.14465100
title: Tasmanian Devil rDNA unit size files

description: analysed_reads file contains raw nanopore reads extracted from a nanopore dataset readsf or the Tasmanian devil (NCBI accession PRJEB34649) in FASTA format used to determine rDNA unit size..<br>Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in FASTA format.<br>Con_indiv_units files contain individual rDNA unit sequences extracted from nanopore reads used to generate the long and short consensus sequence in FASTA format.<br>Consensus_alignment files contains the alignement output in .geneious format.<br>Annotated_Consensus files contains the two annotated consensus sequences in .geneious format.<br>align_Tasmanian_Devil_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (NCBI accession GL000220; see Agrawal & Ganley, 2018).<br>Average rDNA unit size was generated using the included excel spreadsheet.<br>
DOI: 10.17608/k6.auckland.14470983
title: Alignments of Human and Tasmanian devil long and short consensus sequences

description: MAFFT alignments of the Long and Short consensus sequences were generated for the human and Tasmanian Devil to determine where the change in rDNA unit size was occurring in each species.
DOI: 10.17608/k6.auckland.14470983.v1
title: Alignments of Human and Tasmanian devil long and short consensus sequences

description: MAFFT alignments of the Long and Short consensus sequences were generated for the human and Tasmanian Devil to determine where the change in rDNA unit size was occurring in each species.
DOI: 10.17608/k6.auckland.14478324.v1
title: S. cerevisiae consensus sequence generation from nanopore reads

description: Files containing <i>S. cerevisiae</i> consensus sequences generated using alignments of 5, 15 and 25 individual rDNA units, individual rDNA units used to generate the consensus sequence, the raw reads individual rDNA units were extracted from and alignments of consensus sequences to a reference rDNA unit (isolated from a BAC clone NCBI accession U53879.1, isolation and annotations generated by Floutsakou 2013). Alignments of the consensus sequences generated using 5, 15 and 25 rDNA units with each other are included under the "Alignment_of_5_15_25_consensus_sequences" file.
DOI: 10.17608/k6.auckland.14478324
title: S. cerevisiae consensus sequence generation from nanopore reads

description: Files containing <i>S. cerevisiae</i> consensus sequences generated using alignments of 5, 15 and 25 individual rDNA units, individual rDNA units used to generate the consensus sequence, the raw reads individual rDNA units were extracted from and alignments of consensus sequences to a reference rDNA unit (isolated from a BAC clone NCBI accession U53879.1, isolation and annotations generated by Floutsakou 2013). Alignments of the consensus sequences generated using 5, 15 and 25 rDNA units with each other are included under the "Alignment_of_5_15_25_consensus_sequences" file.
DOI: 10.17608/k6.auckland.14478315
title: S. cerevisiae 0.6X Coverage Assembly and rDNA Sequence-Selection Assembly Files

description: Files containing reads selected at random from a Pacbio dataset (NCBI accession PRJEB7245) for a 0.6X Coverage assembly to generate a complete rDNA (S288C_0.66X_assembly_reads.fasta.gz), annotated assembly contig (annotated_rDNA_0.66X_assembly_contig4.geneious), lignment of the complete contig rDNA unit to a reference (U53879.1; RDN37; Chr XII, 2217.. 31308) rDNA unit (Alignment_of_0.6XCoverage_288C_assembly_with_reference).<br>Files containing reads selected by BLAST from a Pacbio dataset (NCBI accession PRJEB7245) to generate assembly of a complete rDNA (S288C_Sequence_Selection_assembly_reads.fasta.gz), annotated assembly contig (S288C_Sequence_Selection_assembly_method_contig1.gb), annotated individual rDNA units (S288C_seqsel_individual_rDNA_units.gb)and alignment of the individual assembled rDNA units to a reference (U53879.1; RDN37; Chr XII, 2217.. 31308) rDNA unit (Alignment_of_SeqSel_units_with_ref.geneious).<br>Alignments to a reference rDNA unit (isolated from a BAC clone NCBI accession U53879.1, isolation and annotations generated by Floutsakou 2013) are available for both assemblies.<br>
DOI: 10.17608/k6.auckland.14478315.v1
title: S. cerevisiae 0.6X Coverage Assembly and rDNA Sequence-Selection Assembly Files

description: Files containing reads selected at random from a Pacbio dataset (NCBI accession PRJEB7245) for a 0.6X Coverage assembly to generate a complete rDNA (S288C_0.66X_assembly_reads.fasta.gz), annotated assembly contig (annotated_rDNA_0.66X_assembly_contig4.geneious), lignment of the complete contig rDNA unit to a reference (U53879.1; RDN37; Chr XII, 2217.. 31308) rDNA unit (Alignment_of_0.6XCoverage_288C_assembly_with_reference).<br>Files containing reads selected by BLAST from a Pacbio dataset (NCBI accession PRJEB7245) to generate assembly of a complete rDNA (S288C_Sequence_Selection_assembly_reads.fasta.gz), annotated assembly contig (S288C_Sequence_Selection_assembly_method_contig1.gb), annotated individual rDNA units (S288C_seqsel_individual_rDNA_units.gb)and alignment of the individual assembled rDNA units to a reference (U53879.1; RDN37; Chr XII, 2217.. 31308) rDNA unit (Alignment_of_SeqSel_units_with_ref.geneious).<br>Alignments to a reference rDNA unit (isolated from a BAC clone NCBI accession U53879.1, isolation and annotations generated by Floutsakou 2013) are available for both assemblies.<br>
DOI: 10.17608/k6.auckland.14479221
title: Diamondback Terrapin rDNA unit sizes

description: Analysed_contigs file contains PacBio contigs from a whole genome assembly of the Diamondback terrapin(PRJNA339452) in FASTA format used to determine rDNA unit size for the Diamondback terrapin.<br>Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in FASTA format.<br>Con_indiv_units files contain individual rDNA unit sequences extracted from PacBio contigs used to generate the consensus sequence in FASTA format.<br>Consensus_alignment files contains the alignement output in .geneious format.<br>Annotated_Consensus files contains the two annotated consensus sequences in .geneious format.<br>align_Diamondback_terrapin_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (Genbank accession X02995).<br>Average rDNA unit size was generated using the included excel spreadsheet.
DOI: 10.17608/k6.auckland.14479221.v1
title: Diamondback Terrapin rDNA unit sizes

description: Analysed_contigs file contains PacBio contigs from a whole genome assembly of the Diamondback terrapin(PRJNA339452) in FASTA format used to determine rDNA unit size for the Diamondback terrapin.<br>Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in FASTA format.<br>Con_indiv_units files contain individual rDNA unit sequences extracted from PacBio contigs used to generate the consensus sequence in FASTA format.<br>Consensus_alignment files contains the alignement output in .geneious format.<br>Annotated_Consensus files contains the two annotated consensus sequences in .geneious format.<br>align_Diamondback_terrapin_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (Genbank accession X02995).<br>Average rDNA unit size was generated using the included excel spreadsheet.
DOI: 10.17608/k6.auckland.14479299.v1
title: Human rDNA unit size

description: Raw_read file contains nanopore reads in FASTA format analysed from a nanopore dataset (PRJNA200694) used to determine rDNA unit size for Humans.<br><br>Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the long and short consensus sequence in FASTA format.<br>Con_indiv_units files contain individual rDNA unit sequences extracted from nanopore reads used to generate the long and short consensus sequence in FASTA format.<br>Consensus_alignment files contains the alignement output in .geneious format.<br>Annotated_Consensus files contains the two annotated consensus sequences in .geneious format.<br>align_Human_long/short_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (NCBI accession GL000220; see Agrawal & Ganley, 2018).<br>Average rDNA unit size was generated using the included excel spreadsheet.
DOI: 10.17608/k6.auckland.14479299
title: Human rDNA unit size

description: Raw_read file contains nanopore reads in FASTA format analysed from a nanopore dataset (PRJNA200694) used to determine rDNA unit size for Humans.<br><br>Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the long and short consensus sequence in FASTA format.<br>Con_indiv_units files contain individual rDNA unit sequences extracted from nanopore reads used to generate the long and short consensus sequence in FASTA format.<br>Consensus_alignment files contains the alignement output in .geneious format.<br>Annotated_Consensus files contains the two annotated consensus sequences in .geneious format.<br>align_Human_long/short_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (NCBI accession GL000220; see Agrawal & Ganley, 2018).<br>Average rDNA unit size was generated using the included excel spreadsheet.
DOI: 10.17608/k6.auckland.14489340
title: Cane toad rDNA unit size

description: Raw read files contain nanopore reads in FASTA format used to determine rDNA unit size for the Cane toad (kindly provided by Dr Richard Edwards of The University of New South Wales, Sydney, Australia).<br>Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the long and short consensus sequence in FASTA format.<br>Con_indiv_units files contain individual rDNA unit sequences extracted from nanopore reads used to generate the long and short consensus sequence in FASTA format.<br>Consensus_alignment files contains the alignement output in .geneious format.<br>Annotated_Consensus files contains the two annotated consensus sequences in .geneious format.<br>align_Human_long/short_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (X02995).<br>Average rDNA unit size was generated using the included excel spreadsheet.
DOI: 10.17608/k6.auckland.14489340.v1
title: Cane toad rDNA unit size

description: Raw read files contain nanopore reads in FASTA format used to determine rDNA unit size for the Cane toad (kindly provided by Dr Richard Edwards of The University of New South Wales, Sydney, Australia).<br>Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the long and short consensus sequence in FASTA format.<br>Con_indiv_units files contain individual rDNA unit sequences extracted from nanopore reads used to generate the long and short consensus sequence in FASTA format.<br>Consensus_alignment files contains the alignement output in .geneious format.<br>Annotated_Consensus files contains the two annotated consensus sequences in .geneious format.<br>align_Human_long/short_con_with_ref file contains the rDNA consensus sequence aligned to a reference sequence (X02995).<br>Average rDNA unit size was generated using the included excel spreadsheet.
DOI: 10.17608/k6.auckland.14489484
title: RepeatMasker analysis of Human long and short consensus sequences.

description: RepeatMasker outpus (RM2_Human..._IGS.align) were used to annotate the long and short human rDNA consensus units (Repeat_annotated_Human_rDNA_consensus_long/short.geneious) generated using nanopore reads (NCBI accession PRJNA200694).The repeat-annotated long and short consensus sequences were aligned to compare repeat number, size and position (Human_Long_Consensus_aligned_with_Human_Short_Consensus).
DOI: 10.17608/k6.auckland.14489484.v1
title: RepeatMasker analysis of Human long and short consensus sequences.

description: RepeatMasker outpus (RM2_Human..._IGS.align) were used to annotate the long and short human rDNA consensus units (Repeat_annotated_Human_rDNA_consensus_long/short.geneious) generated using nanopore reads (NCBI accession PRJNA200694).The repeat-annotated long and short consensus sequences were aligned to compare repeat number, size and position (Human_Long_Consensus_aligned_with_Human_Short_Consensus).
DOI: 10.17608/k6.auckland.14489490.v1
title: RepeatMasker analysis of Tasmanian devil long and short consensus sequences

description: RepeatMasker outputs (RM2_Tasmanian_devil.._IGS.align) were used to annotate the long and short human rDNA consensus units (AnnotatedTasmanian_devi_rDNA_consensus_long/short.geneious) generated using nanopore reads (NCBI accession PRJEB34649).The repeat-annotated long and short consensus IGS sequences were aligned to compare repeat number, size and position (Tasmanian_Devil_Long_Consensus_aligned_with_Tasmanian_Devil_Short_Consensus).
DOI: 10.17608/k6.auckland.14489490
title: RepeatMasker analysis of Tasmanian devil long and short consensus sequences

description: RepeatMasker outputs (RM2_Tasmanian_devil.._IGS.align) were used to annotate the long and short human rDNA consensus units (AnnotatedTasmanian_devi_rDNA_consensus_long/short.geneious) generated using nanopore reads (NCBI accession PRJEB34649).The repeat-annotated long and short consensus IGS sequences were aligned to compare repeat number, size and position (Tasmanian_Devil_Long_Consensus_aligned_with_Tasmanian_Devil_Short_Consensus).
DOI: 10.17608/k6.auckland.14489493.v1
title: RepeatMasker analysis of Mouse (Mus muscularis) IGS transposons

description: RepeatMasker outputs (RM2_corrected_Mouse.._IGS.align) were used to annotate a Mouse IGS sequence extracted from a consensus unit (Genbank accession BK000964.3) (Repeat-annotated_Corrected_Mouse_rDNA.geneious).
DOI: 10.17608/k6.auckland.14489493
title: RepeatMasker analysis of Mouse (Mus muscularis) IGS transposons

description: RepeatMasker outputs (RM2_corrected_Mouse.._IGS.align) were used to annotate a Mouse IGS sequence extracted from a consensus unit (Genbank accession BK000964.3) (Repeat-annotated_Corrected_Mouse_rDNA.geneious).
DOI: 10.17608/k6.auckland.14489742
title: Chimpanzee PacBio assembly

description: Files containing PacBio reads selected by BLAST to generate assembly of a complete rDNA (Chimpanzee_rDNA_assembly_reads.fasta.gz), annotated assembly contig (annotated_Chimpanzee_seqsel_assembly_method_contig.geneious), annotated complete assembly (annotated_Chimpanzee_seqsel_rDNA.geneious).<br>Alignment of the complete contig rDNA unit to a reference gene (KX061886):(align_Chimpanzee_seqsel_assembly_with_ref_KX061886.geneious)
DOI: 10.17608/k6.auckland.14489742.v1
title: Chimpanzee PacBio assembly

description: Files containing PacBio reads selected by BLAST to generate assembly of a complete rDNA (Chimpanzee_rDNA_assembly_reads.fasta.gz), annotated assembly contig (annotated_Chimpanzee_seqsel_assembly_method_contig.geneious), annotated complete assembly (annotated_Chimpanzee_seqsel_rDNA.geneious).<br>Alignment of the complete contig rDNA unit to a reference gene (KX061886):(align_Chimpanzee_seqsel_assembly_with_ref_KX061886.geneious)
DOI: 10.17608/k6.auckland.14489748
title: Alignment of repeat-annotated Mouse IGS to repeat-annotated Human IGS ransposons

description: Alignment of the human long repeat-annotated IGS sequence to the mouse repeat-annotated sequence (Modified from BK000964.3) to identify differences in repeat number, type and length.
DOI: 10.17608/k6.auckland.14489748.v1
title: Alignment of repeat-annotated Mouse IGS to repeat-annotated Human IGS ransposons

description: Alignment of the human long repeat-annotated IGS sequence to the mouse repeat-annotated sequence (Modified from BK000964.3) to identify differences in repeat number, type and length.
DOI: 10.17608/k6.auckland.14491056
title: HiHi rDNA unit Measuring Spreadsheet

description: Excel spreadsheet used to calculate the rDNA unit size of the HiHi from a BLAST output of nanopore reads. The BLAST output used to generate this spreadsheet was kindly provided by Dr Annabel Whibley of the University of Auckland.