Genome Browser
Browse the
Hydra 2.0 genome assembly, protein models, RNA-seq data, and other genome annotation using the
JBrowse genome viewer.
Search
OR
The following tracks are currently available for viewing:
- Aligned ATAC-seq tracks
- Aligned ATAC-seq reads as quantitative data in an x/y plot. ATAC-seq reads (replicate 1, 2, and 3) were generated for whole homeostatic Hydra. The Juliano_whole_peaks track is a consensus peak track consisting of all peaks that passed an IDR threshold of 0.1 for at least one pairwise comparison among the three biological replicates (Juliano_whole_rep1-3).
Aligned ATAC-seq reads from Murad et al. 2019 from adult tissues and regeneration time points 0-48h. Reads were aligned to the Hydra 2.0 genome using bowtie v. 1.2.
- Aligned ChIP-seq tracks
- Aligned ChIP-seq reads from Murad et al. 2019 from whole Hydra, Hydra head and regeneration time points 0-24h. Reads were aligned to the Hydra 2.0 genome using bowtie v. 1.2.
- Aligned RNA-seq tracks
- RNA-seq reads from Petersen et al. 2015 (Molecular Biology and Evolution) from time points 0-48h were aligned to the Hydra 2.0 genome using HISAT2. Aligned reads tracks display all aligned RNA-seq reads. BigWig XY tracks display the aligned RNA-seq reads as quantitative data in an x/y plot.
- Aligned RNA-seq reads from Murad et al. 2019 from adult Hydra hypostome, tentacles, body column, budding zone and foot, also from regeneration time points 0-48h and budding stages 1-10. Reads were aligned to the Hydra 2.0 genome using bowtie v. 1.2.
- Juliano_Trinity
- RNA-seq reads from Juliano et al. 2014 (PNAS) were assembled into Trinity transcripts. The Trinity assembled transcripts were aligned to the Hydra (2.0) genome using Splign.
- Juliano_aepLRv2
- Transcripts from a transcriptome assembly for Hydra vulgaris AEP (38,749 transcripts) were aligned to the Hydra 2.0 genome using Splign.
- Petersen_Trinity
- RNA-seq reads from Petersen et al. 2015 (Molecular Biology and Evolution) from time points 0–12 h were used to assemble a de novo transcriptome, which consists of 36,338 high quality transcripts. The Trinity assembled transcripts were aligned to the Hydra (2.0) genome using Splign.
- AUGUSTUS
- Hydra 2.0 gene models predicted using AUGUSTUS.
- AUGUSTUS_unmasked
- Hydra 2.0 gene models predicted using AUGUSTUS with the unmasked genome.
- FGENESH
- Hydra 2.0 gene models predicted using FGENESH.
- PASA
- RNA-seq reads from Juliano et al. 2014 (PNAS) were assembled into Trinity transcripts. Transcripts were used to create gene structures based on spliced alignments with PASA.
- Hydra1.0_JGI
- Hydra 1.0 gene models (from JGI) aligned to the Hydra 2.0 genome assembly using Splign.
- Hydra1.0_NCBI
- Hydra 1.0 gene models (from NCBI) aligned to the Hydra 2.0 genome assembly using Splign.
- BLASTP_augustus_vs_NCBI_nr
- BLASTP results from using AUGUSTUS protein models as queries against the NCBI nr protein database with an e-value cutoff of 1e-5.
- BLASTP_augustus_vs_UniProt
- BLASTP results from using AUGUSTUS protein models as queries against the UniProt protein database with an e-value cutoff of 1e-5.
- PASA_coding_regions
- Candidate coding regions identified from PASA gene structures by TransDecoder.
- AUGUSTUS_PFAM
- Hydra 2.0 protein domains derived from PFAM HMMscans with an e-value cutoff of 1e-6 using the AUGUSTUS datasets.
- 6FRAMES_PFAM
- Hydra 2.0 protein domains derived from PFAM HMMscans with an e-value cutoff of 1e-6 using the six-frame translations of the Hydra 2.0 genome.
- Reference Sequence
- The Hydra 2.0 genomic sequence and corresponding six-frame translations depicted when fully zoomed-in.
- MASK
- Genomic regions that have been masked using RepeatMasker and RepeatModeler are highlighted in light blue.
- SCF
- Assembled genomic scaffolds (SCF) appear as solid black tracks with intermittent gaps shaded bright pink.