At a glance
- Save genes with selected annotations directly into Photo51 for primer design and cloning.
- Compare CRISPR target sites by their scores, with known variants alongside, and pick your guides.
- Find genomes and tracks from UCSC, NCBI, Ensembl and ENCODE in one search.
- Browse faster, and offline, by downloading the genomes you use most in the desktop app.
Finding a gene is one step. Working with it is the next. Photo51 connects genome browsing with sequence design and cloning, so you can save genes with their annotated features, compare CRISPR guide RNAs and use the sequences directly in your design.
We’ve redesigned the Genome Browser around this whole path, from finding a genome to working with its sequence.
Go from the genome to your design, in one program
Save a gene or any region you select, and it goes straight into your Photo51 library. You choose which genes, guides and variants to keep, and they arrive already labeled, so you do not have to recreate those annotations by hand. Add flanking sequence at either end if your design needs it.
From there it’s a sequence like any other in Photo51. Design primers for it, use it in your cloning workflows, or build a plasmid around it, without exporting a file and starting again in another program.
Compare guide RNAs alongside known variants
Picking a guide means optimizing efficiency, specificity, off-target binding and checking for known variants. The CRISPR/Cas9 track shows candidate Cas9 target sites in the region you’re viewing, and the SNP track shows known variants alongside them, next to the exons of your gene.
Save the region, and the target sites come into your sequence as candidate guide RNAs, color-coded by their efficiency and specificity scores. Compare them, quickly check for known variants, and mark the ones you choose as picked, so you can find them again later.
Step by step: how to find guide RNAs and their scores in Exporting CRISPR and SNP Tracks in Photo51.
Find genomes and tracks in one search
You do not need to know which database holds the genome or annotation you want. Search genomes from UCSC, NCBI and Ensembl, including more than 52,000 assemblies from UCSC and its Genome Archive (GenArk), and tracks from collections including ENCODE, GTEx and 1000 Genomes. Before you add a genome, Photo51 tells you if anything is missing, such as cytobands.
Every genome and track you add goes into your own library, so the ones you rely on are a click away, and you only search for them once. Someone mapping regulatory elements needs different annotation from someone picking CRISPR targets, so you switch on only the tracks that matter for each experiment.
See how to search for, add and download genomes and tracks in Importing and Downloading Genomes and Tracks in Photo51.
Browse faster. Keep working offline
Move quickly between genes and tracks with a fast, responsive Genome Browser. Save what you need locally to continue offline.
For the genomes and tracks you use often, we recommend downloading them in the Photo51 desktop app. They then load from your own computer, so browsing is noticeably faster and keeps working without an internet connection. Downloading is optional, and you can remove the local copy at any time.
Read more about the new Genome Browser introducing the New Genome Browser
Search by gene, alias or genome name
Search for a gene by its symbol or alias. An ideogram shows every chromosome at a glance, and as you zoom in, the chromosome stays above your view so you always know where you are.
Find out more about navigating the Photo51 Genome Browser Navigating the Genome Browser, from the ideogram to a single gene.
Frequently asked questions
Can I use the Photo51 Genome Browser offline?
Yes, in the Photo51 desktop app if you have downloaded genomes and tracks you can use them offline as well.
Which databases does the Photo51 Genome Browser search?
Genomes from UCSC, including the UCSC Genome Archive (GenArk), NCBI and Ensembl. Tracks from the UCSC track catalog and from collections by NCBI, Ensembl, ENCODE, GTEx, the 4D Nucleome project and 1000 Genomes.
Does it show CRISPR guide RNA scores?
Yes. The CRISPR/Cas9 track shows Cas9 target sites with an NGG PAM. When you save a region into Photo51, each candidate guide RNA shows its Doench 2016 and Moreno-Mateos efficiency scores, its MIT specificity score and its out-of-frame score.
Can I upload my own genomes and tracks?
Yes. Upload your own genome or track files and they appear in your library alongside the ones from public databases.
How large a region can I save?
You can save regions of up to 10 Mb into your Photo51 library.
Is the Photo51 Genome Browser free to use?
Yes. Create a free Photo51 account and you can use the Genome Browser straight away. To save genes, regions and guide RNAs into your Photo51 library, you need a Photo51 subscription.
Photo51 Genome Browser guides
- Navigating the Genome Browser Navigating the Genome Browser
- Importing and Downloading Genomes and Tracks in Importing and Downloading Genomes and Tracks
- Exporting CRISPR and SNP Tracks in Exporting CRISPR and SNP Tracks
The redesigned Genome Browser is available in Photo51 now. If there’s a genome, track or workflow you’d like us to support, write to feedback@fearlessleague.com .
Try the Genome Browser in Photo51
Have a question we haven’t covered? Check the Photo51 FAQ Photo51 FAQ.