Frequently Asked Questions (FAQ)

• Can I have a free trial?
  • Our 30-day money back guarantee offers the equivalent of a free trial, no questions asked: cancel within 30 days and it will have cost you nothing.
  • If you are unable to put the 1 month charge onto your account, please fill out this pre-written email request form.
• Do you offer discounts for students or for academic researchers?
  • Yes, we currently do.
  • If you are a student, you can subscribe to a solo plan at half price using the discount code Student50off. Within ten days of signing up, please send us an email with a photo of your student id.
  • For other academics, we provide a 25% discount for solo, group, and small public subscriptions if your lab's consumables and equipment budget is less than 50,000 euros annually. Use discount code LowIncomeAcademia. Subsequently, please send us an email self-certifying that the lab fulfills the expenditure criterion.
• Who uses SequenceServer Cloud?
  • Our customers include international companies from the biotech, pharma and agroindustry sectors, non-profit organizations, academic and governmental research laboratories, and students.
• How secure it this?
  • Protection of our customers' data is extremely high priority. We use reasonable organizational and technical measures designed to prevent unauthorized access, use, alteration or disclosure of data that customers entrust us with. Access to servers, code, accounts, and data is managed on "need-to-know" "need-to-access" bases. Data are encrypted and siloed wherever possible. We only use highly trusted software and service dependencies with rigorus security policies and track records. We can provide more security information under NDA. We are obtaining the UK Government's Cyber Essentials certification. If your organization would require SOC2 certification, please contact us.
• How stable is SequenceServer Cloud? Will my BLAST instance always be accessible?
  • We provide a stable, reliable, and secure cloud BLAST service. Our customers rely on our service being available worldwide at all times. This is key to our success and a main aim of our service. We target 100% uptime, and our track record is in line with this. Very occasionally (i.e., up to a few times per year), we must momentarily take our service offline for critical updates. Such updating takes between a few seconds and a few minutes, and when it is needed, we avoid times of high demand. The infrastructure we use is highly reliable and redundant.
• How do I provide my sequence databases?
  • Your SequenceServer instance has a graphical administrator dashboard that allows you to upload sequence databases from your local computer or from another machine. You can upload individual FASTA files (raw or .gz or .zip compressed), formatted BLAST databases, or archives (.zip or .tar.gz) of multiple FASTA files or databases.
  • We will appropriately format each FASTA file into a BLAST database.
  • You could also provide a Dropbox/Google Drive share, or a set of http or ftp links. If, for example, you have your data in DropBox, generating that type of link is easy. Finally, we can provide a secure AWS/S3 or ftp upload link.
• What if I want a database to have a different title than its filename?
  • First, we do some automatic cleaning and clutter removal. We converting all '_' and '-' to spaces, and remove extensions such as ".fasta" or ".fa".
  • But if you want to change your database names even more, the easiest is to rename your fasta files before uploading them. Alternatively, you can specify the display name in the upload interface. If you want to do things in an automated fashion, you can alternatively provide a .title file alongside your fasta file. For example if your genome assembly is `Best_species_masurca_2021-11-yw.fasta`, the accompanying file can be `Best_species_masurca_2021-11-yw.fasta.title`. That .title file should simply include the text you want to use as a title, for example Best species genome 1.0. This can be handy if you're uploading many files
  • The administrator dashboard also lets you rename existing databases (however, due to BLAST's internals, this can take a few seconds to minutes).
• How many databases can I include? How many BLAST analyses can I run?
  • Do what you want: we have no hard limits on numbers of databases, blast searches, or query sizes.
  • However, we must have a fair usage policy to ensure quality of service for all users. Most people need not worry, just like you don't worry about the fair usage policy of your internet or mobile phone providers. An example of a setup that would go against our fair usage policy could be to run BLAST of 10,000,000 queries against the NCBI NR every few days (and anyways BLAST is unlikely to be the most appropriate algorithm for that type of search).
  • If you're unsure about your scenario, please don't hesitate to reach out.
• What do I need to do to add, remove, or change genomes, proteomes or transcriptomes? What about adding/removing users? How often often can I update databases or users?
  • We have a graphical user interface dashboard that enables the administrator of an instance to easily add and remove databases and users. Some screenshots here
  • You can make as many changes as you want, as often as you want.
• Which versions of SequenceServer and BLAST does the cloud service use?
  • We run the latest stable version of SequenceServer 2. and of NCBI BLAST+. We continually roll out upgrades so your analyses benefit from the highest sensitivity, specificity, visualizations and download options.
  • We know that for specific projects it can be helpful to freeze your analyses to specific versions of BLAST and SequenceServer. Get in touch if you need this.
• Can I go back to a previous BLAST result?
  • Yes, BLAST search results remain at their URL - the https address at the top of the page. How long the results are retained for depends on your plan: 7 days for Solo, 30 days for the Group plan and for public databases, one year for Pro and Business subscription plans.
• Can I share my BLAST results?
  • Feel free to share the https URL at the top of the page with others who also have access to your password-protected BLAST instance. Alternatively, save your BLAST report using the built-in functionality of your web browser (save as a PDF or as a Web archive). Additionally, you can export the raw data (in table or XML formats). Finally, you can easily download figures from the BLAST report in publication ready PNG or SVG formats.
• How will I access my SequenceServer?
  • Through a web browser, at https://any_name_you_can_think_of.sequenceserver.com (with dashes, or underscores or not - as long as nobody else is using it.
  • For subscription plans with full custom domain integration, we can use a subdomain on your toplevel domain, for example https://blast.growbetterplants.com, or we can also host in what appears to be a subfolder of your main site, e.g. https://bigcheeselab.org/blast, while you host the rest of the site.
• Do I need to sign in every time I want to do a BLAST search?
  • No, we use a cookie in your browser to remember that you previously logged in successfully.
• Is it possible to further restrict access to a private SequenceServer instance?
  • Yes, we can, for example, additionally restrict access based on a range of IPs or add http password authentication.
  • Subscription plans with single-sign-on (SSO) support rely on the criteria specified by the IT administrators managing SSO rules. We can work with identity providers including Azure, okta, onelogin, SAML, Google, ADFS, PingIdentity and OpenID
  • We can also offer dedicated servers whereby none of our other customers would access the physical server or filesystem that your data are on. Costs are from $599 per month, and depend on the size of the server and its geographical location (e.g., some customers may prefer to keep data in the European Union (EU)).
• Can I get a dedicated server?
  • Most of our users are happy to use a dedicated instance, served at https://myserver.sequenceserver.com. However, some enterprise customers prefer to have completely dedicated infrastructure. This is possible. Please reach out.
• Can I block downloads from my site?
  • Sometimes, a database administrator doesn't want all sequences in the database to be downloadable. If you want us to block downloads, just open a support ticket. Users will still be able to see database versions of HSP alignments, but downloading of entire hit sequences from the database will be impossible.
• I run the aardvarkgenomes.org web site. Could I embed a hosted SequenceServer in my web page?
  • Yes, if we run aardvarkgenomes.sequenceserver.com, there are essentially four manners through which you can integrate it with your website. We can help with each of them
  • First, you can simply use iframe embedding. This works (surprisingly well).
  • Second, you can change DNS records to make blast.aardvarkgenomes.org, or even simply aardvarkgenomes.org be synonymous with aardvarkgenomes.sequenceserver.com. We can change the identity of what we are serving so it reflects the name you prefer.
  • Third, we can pass information on the server side, by modifying your webserver's configuration file. If, for example you are running nginx, you can use its reverse proxy features. So if you want the blast interface served under https://aardvarkgenomes.org/blast, then you would put the following into your nginx.conf:

                                    location /blast/ {
                                      proxy_pass https://aardvarkgenomes.sequenceserver.com/;
                                      proxy_connect_timeout 15;
                                      proxy_read_timeout 240;
                                    }
                                  

  • In that way, everything goes through your server, but the interface appears to your website users as if its served from your site directly.
  • Finally, we can host your normal aardvarkgenomes.org pages as well. Thus you don't need a separate webserver or hosting provider (see also next question).
• Can you host normal web pages too?
  • Yes, we can. Say you are hosting a community or departmental web page and want to enable your users to also download fasta files or protocols, view images, or access a jBrowse genome browser or other data. We are now able to also host such pages and data on our servers. Yes it works for static html pages, or for dynamic content (e.g., PHP/Lamp).
  • So for example, you could have https://myorganismbase.com as a normal website, and https://myorganismbase.com/blast for SequenceServer searches. For small-scale usage (less than 5GB data) there is no extra cost for this on annual subscription plans.
  • Please get in touch with your constraints if this is something you'd like to pursue.
• Can you give me a quote for a grant proposal or to submit a purchase order through my finance department?
  • Yes. Get in touch with us, and let us know which plan and duration you want the quote to cover. We will get a quote back to you rapidly.
  • We can only process purchase orders if the spend is $500 or more, and we are unable to provide discounts for orders placed via purchase order. This is due to the high costs of processing such orders.
• Do you take other payment mechanisms?
  • If payment by bank card, Apple Pay or Google Pay doesn’t work for you, please get in touch.
  • Some finance departments require going through a purchase order process. Because this has substantial administrative overhead on our side, we can only do it for subscriptions of at least one year. Have your finance department contact us at contact@sequenceserver.com to get our details.
• Can I prepay for several years?
  • Yes - we understand that the need for this can arise. We offer an additional 10% discount for multi-year subscriptions. Please get in touch by email with your specific request and preferred payment mechanism, and we will rapidly get back to you.
• Is the payment mechanism secure?
  • We take security extremely seriously. SequenceServer doesn’t want or need your payment information. Instead, we process payments using the industry standard Stripe.com. You can thus pay with Apple Pay, Google Pay, or by bank card. Stripe annually process hundreds of billions of dollars in payments, including for Kickstarter, Booking.com, Zoom, Uber, Deliveroo and Unicef.
• Can I cancel my subscription?
  • Yes. We will refund everything if you cancel in the first 30 days. If you cancel after the first 30 days, your subscription will terminate at the end of your current billing period (month or year).
  • If you would like to cancel, you can do it directly through your administrator dashboard. No questions asked.
• Is there a cancellation fee?
  • No, there are no cancellation fees or charges. We will refund you the whole amount if you cancel in the first 30 days. If you cancel after the first 30 days, your subscription will simply not renew at the end of your current billing period.
• I have other questions. How do I get in touch with you?
  • Feel free to contact us by email. We are also happy to arrange a demonstration or question/answer call over zoom.
• Can I have a demonstration? Or can we discuss our custom needs?
• Yes. Book a time here. If none of those times work, please write us an email with your availabilities.