With Open Access, you can use the Photo51 Genome Browser for free to explore genomes, search for genes and view annotation tracks. All you need is a free Photo51 account. Everything inside the Genome tab is open to browse, while saving genes and regions back into your Photo51 library requires a subscription.
Open Access (free) | Subscription | |
Browse genomes, chromosomes and genes | Yes | Yes |
Search and view genomes and tracks | Yes | Yes |
Download genomes and tracks (desktop app) | No | Yes |
Save genes and regions into your Photo51 library | No | Yes |
Compare, pick guideRNAs, set up cloning | No | Yes |
Navigating the Genome Browser (Included in Open Access)
When you open the Genome tab in the top banner, the browser loads the Homo sapiens hg38 ideogram (karyogram), along with the RefSeq Select track. From here, you have access to all browsing and navigation tools:
- Click any chromosome in the ideogram (karyogram) or use the search bar at the top left to jump to a specific gene. Click Whole genome at the top right to return to the overview.
- Click a gene in the browser (it turns red) to see its location, length and number of exons and introns , or click Focus gene in the top ribbon to bring the entire gene into frame.
- Zoom in and out, down to individual nucleotides, with the top zoom slider or by double-clicking. Pan along the chromosome by dragging the blue window in the ideogram (karyogram) at the top, and switch the crosshairs, center line and track labels on or off in the top ribbon.
For more detail, see Navigating the Genome Browser Navigating the Genome Browser
Managing Genomes and Tracks (Included in Open Access)
You can choose which reference genomes and annotation tracks are displayed from the left sidebar:
- Genomes: Use the Genome dropdown to switch assemblies or click the cog icon next to Reference genome to open the genomes window. Here you can manage My Genomes library, search for new assemblies under Search Genomes to add them to your library. .
- Tracks: Select tracks from the Choose tracks dropdown and drag the three-line handle next to each track in the left sidebar to change their order. Click the cog icon next to tracks to open the tracks window, where you can manage My Tracks Library, search for and add new tracks, such as CRISPR/Cas9 -NGG Targets or Common dbSNP.
- Offline Downloads (desktop app only): If you’re using the Photo51 desktop app, you can click Download next to any genome or track in your library to store a local copy on your computer for faster browsing.
For more detail, see Importing and Downloading Genomes and Tracks
Saving to the Sequence Viewer (subscription only)
You can inspect genes, SNPs and CRISPR target sites in the Genome Browser for free. Saving a gene or region inot your Photo51 library as an editable sequence requires a Photo51 subscription. With a subscription, you can:
- Save a gene from its information box or with Save gene in thetop banner
- Save any region by holding Shift, dragging across it and clicking Save sequence in the top banner
- Sequence Export Options: Add 5’ and 3’ flanking sequences, reverse complement the sequence, and number exons and introns automatically as you save.
- Analyze CRISPR Guides and SNPs in Sequence View: Open the saved sequence to compare color-coded guide RNAs, check their scores: Doench ’16 efficiency, MIT specificity, Moreno-Mateos efficiency, Out-of-frame, and Doench ’14 efficiency. You can alsocheck SNP overlaps and filter and select guides in the Guide RNAs table at the bottom.
See How to Find Guide RNAs and Their Scores in Photo51 for the full workflow.
Related
- The Photo51 Genome Browser
- Navigating the Genome Browser
- Importing and Downloading Genomes and Tracks
- How to Find Guide RNAs and Their Scores in Photo51
- What’s new in the Photo51 Genome Browser