The new Photo51 Genome Browser brings genome exploration into the same app you use for sequence design. Find a gene or region, explore its annotations, variants, CRISPR targets and other data tracks. Save the sequence to continue your work in Photo51, without exporting or importing files. A clear interface and fast loading help you move through the data. In the desktop app, you can also download genomes and tracks for faster local access and offline work. Here’s what’s new, and how it can fit into your workflow.
For an overview of what you can do with it, see our Photo51 Genome Browser overview.
From Genome to Sequence Design
Move directly from a reference genome to a sequence file in Photo51. Click a gene to see its length and the number of exons and introns, then save the gene. You can also save any region of DNA up to 10 Mb by holding Shift and dragging across it.
When you save, you can:
- Flanking sequence at the 5’ and 3’ ends, for example to include a promoter or regulatory region
- Save the reverse complement
- Number the exons and introns automatically
- Include known SNPs and CRISPR/Cas9 NGG targets from your open tracks as features
Your saved sequence is then available in Photo51 for whatever comes next, for example:
- Cloning: use the gene or region as the starting point for expression, reporter or other constructs.
- PCR and primer design: work from the extract genomic sequence, with exons, introns and flanking regions clearly marked.
- Checking variants: see where known SNPs fall, for example, before choosing primer sites or comparing with your own sequencing data.
- Gene editing: compare CRISPR guides by their scores and pick the ones you want to use.
Note: Saving sequences into your Photo51 library requires a Photo51 subscription.
For a step-by-step example of saving a gene and working with guide RNAs, see Exporting CRISPR and SNP Tracks.
A Clear, Focused Interface
Everything you need to move around the genome sits in one view:
- Sidebar: Shows your reference genome, chromosome and open tracks. Add a genome or track from the same place.
- Karyogram (ideogram): Shows all chromosomes side-by-side. Click a chromosome to open it.
- Chromosome karyogram (ideogram): Shows you where you are on the chromosome and lets you move along it.
- Whole genes: Click a gene and select Focus gene to bring it completely into view.
- Any region: Hold Shift and drag to select any stretch of DNA, from part of a gene to several genes at one.
- Tracks: Pan across a region, drag tracks to reorder them and switch each track between expanded, squished and collapsed
To go to a gene or position, use one of two searches:
- Gene search: accepts names, symbols and aliases.
- Locus search: Enter coordinates directly. Coordinates outside the chromosome trigger an explanation so you can correct them.
- Adjust your view: Pan across a region, drag tracks into a different order and choose how much detail each track displays.
See the Genome Browser Navigation guide for controls and track display options.
Fast Loading and Offline Access
The human genome opens with one gene track, RefSeq Select, so you can start without waiting for additional annotations to load.
In the Photo51 desktop app, you can download genomes and tracks you use most often. Local copies load from your computer instead of streaming over the internet, for faster access during repeated use and continued work offline.
- Manage downloads: pause, resume or cancel a download. Interrupted downloads continue from where they stopped.
- Search offline: gene search also works on genomes you’ve downloaded, even without an internet connection.
- Check what’s local: downloaded genomes and tracks are marked with a Local tag, and you can filter your library whether they are stored locally or in the cloud.
- Free up space: remove local copies when you no longer need them.
Note: Downloading genomes and tracks is only available in the Photo51 desktop app, not in Photo51 in your web browser.
Find the Genomes and Tracks You Need
Search for genome assemblies and tracks you need and add them to your Photo51 libraries, ready to select from the sidebar.
Find your genome: Search Genomes brings together results from:
- UCSC Genome Archive (GenArk)
- NCBI
- Ensembl.
UCSC and GenArk alone provide access to more than 50,000 assemblies, covering familiar model organisms to less-studied species.
You do not need to know the exact assembly name to start a search. For example, hg38, GRCh38, human or Homo sapiens can all help you find the human reference genome. Choose an assembly you need and add it to My Genomes Library to make it available in the sidebar.
Add the Tracks You Need
These tracks are available by default from the Choose tracks dropdown in the left sidebar:
- RefSeq Curated
- RefSeq All
- MANE
- ClinVar dbSNPs
- CRISPR Targets
To find more, click on the cog icon to open the Tracks window and search the Track catalogue. Any track you add appears in My Tracks Library, ready to select from the sidebar.
Search Tracks gives you access to the UCSC track catalog and additional collections from research consortia and databases:
- GTEx: the GTEx Analysis Hub and single-tissue eQTLs
- NCBI: ALFA allele frequencies, dbVar structural variants and RefSeq Functional Elements
- Ensembl: the Ensembl Regulatory Build
- ENCODE: ChIP and other signal tracks
- 4DN: tracks from the 4D Nucleome project
- 1000 Genomes: low-coverage alignments
Available tracks depend on the selected genome assembly. Most of these collections t cover human, and some also available for mouse and other model organisms.
Try the Genome Browser
- Open Photo51 and go to the Genome tab in the top ribbon.
- Human (hg38) is already in My Genomes Library, with RefSeq Select open.
- Choose another genome or add tracks from the sidebar to explore the data you need.
For account requirements and subscription features, see Open Access in the Genome Browser.
Can’t find a genome, or have a question about the Genome Browser? Drop us a line in the Help & Community tab in Photo51, or email us at: feedback@fearlessleague.com.