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13 datasets found
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Brown snake and Tiger snake rDNA unit size files
The University of AucklandRaw 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). Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in...Created 1 May 2021 • Updated 27 March 2025 -
Golden-fronted woodpecker rDNA unit size files
The University of AucklandGFW_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. GFW_con_reads file contains raw nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in FASTA format for...Created 1 May 2021 • Updated 27 March 2025 -
Tuatara rDNA unit size files
The University of Aucklandreads_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.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...Created 1 May 2021 • Updated 27 March 2025 -
S. cerevisiae consensus sequence generation from nanopore reads
The University of AucklandFiles containing S. cerevisiae 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,...Created 1 May 2021 • Updated 27 March 2025 -
S. cerevisiae 0.6X Coverage Assembly and rDNA Sequence-Selection Assembly Files
The University of AucklandFiles 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.....Created 1 May 2021 • Updated 27 March 2025 -
Diamondback Terrapin rDNA unit sizes
The University of AucklandAnalysed_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. Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the consensus sequence in FASTA format. Con_indiv_units...Created 1 May 2021 • Updated 27 March 2025 -
Human rDNA unit size
The University of AucklandRaw_read file contains nanopore reads in FASTA format analysed from a nanopore dataset (PRJNA200694) used to determine rDNA unit size for Humans. 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. Con_indiv_units files contain individual rDNA unit...Created 1 May 2021 • Updated 27 March 2025 -
Cane toad rDNA unit size
The University of AucklandRaw 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). Con_reads files contain raw nanopore reads individual rDNA unit sequences were extracted from to generate the long and short consensus sequence in FASTA...Created 1 May 2021 • Updated 27 March 2025 -
RepeatMasker analysis of Human long and short consensus sequences.
The University of AucklandRepeatMasker 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...Created 1 May 2021 • Updated 27 March 2025 -
RepeatMasker analysis of Tasmanian devil long and short consensus sequences
The University of AucklandRepeatMasker 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...Created 1 May 2021 • Updated 27 March 2025 -
Chimpanzee PacBio assembly
The University of AucklandFiles 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). Alignment of the complete contig rDNA unit to a reference gene...Created 1 May 2021 • Updated 27 March 2025 -
Alignment of repeat-annotated Mouse IGS to repeat-annotated Human IGS ransposons
The University of AucklandAlignment 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.Created 1 May 2021 • Updated 27 March 2025 -
Platypus PacBio assembly
The University of AucklandFiles containing PacBio reads selected by BLAST to generate assembly of a complete rDNA (Platypus_rDNA_assembly_reads.fasta.gz), annotated assembly contig (Platypus_sequence_selection_assembly_annotated_contig_3.geneious), annotated complete assembly (Platypus_complete_rDNA_Sequence_Selection_Assembly.geneious) and partial units...Created 1 May 2021 • Updated 27 March 2025
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