REST API

Cohen Emiliano

unread,

Jun 19, 2025, 12:35:00 PMJun 19

to UCSC Genome Browser Public Support

Dear UCSC Genome Browser Support Team,

I'm writing because I have a problem with BLAT on the UCSC Genome Browser, which I use a lot for my research. Since today, my programs can't connect, and instead of the BLAT results, I get this message:

HTML

<html><head> <script> function showWidget() { turnstile.render('#myWidget', { sitekey: '0x4AAAAAABgxfUUSzYakb-Pd', theme: 'light', callback: function (token) { const parser = new URL(window.location); parser.searchParams.set('token', token); window.location = parser.href; }, }); } </script> </head><body> <style>body, h1, h2, h3, h4, h5, h6 { font-family: Helvetica, Arial, sans-serif; }</style> <h4>The Genome Browser is protecting itself from bots. This will just take a few seconds.</h4> <small>If you are a bot and were made for a research project, please contact us by email.</small> <script src='https://challenges.cloudflare.com/turnstile/v0/api.js?onload=showWidget' async defer></script> <div id='myWidget'></div> </body></html>

My research depends a lot on using BLAT automatically. I use it for checking my primer sequences. This problem is really stopping my work.

Could you please tell me the best way for researchers like me to use BLAT with a program now? Is there a way to allow my computer to access it for my research?

Thank you for your help.

Sincerely,

Emiliano Cohen, PhD

Luis Nassar

unread,

Jun 23, 2025, 6:58:21 PMJun 23

to Cohen Emiliano, UCSC Genome Browser Public Support

Hello, Emiliano.

As you've probably noticed, the service became available again last week. However, we will soon reinstate the CAPTCHA requirement (~2.5 weeks). We'll note down your contact information and reach out before the change goes live to provide you with a user agent you can use to bypass the CAPTCHA.

To give you some context, we have been battling exponential increases in bot traffic. Now, with LLM crawlers, we have no choice but to enforce a CAPTCHA site-wide.

We'll be in touch soon.

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/2017088c-744c-4ba5-afa8-592ac7539743n%40soe.ucsc.edu.

--

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

Maximilian Haeussler

unread,

Jun 24, 2025, 5:27:29 AMJun 24

to Luis Nassar, Cohen Emiliano, UCSC Genome Browser Public Support

Hi Emiliano,

do you know that we provide a "blat" command line program that runs blat locally on your computer, which is a lot faster when running many primers than our API? We also have a gfClient command line tool that accesses our servers directly. And we have the isPcr tool, which may be better for checking primers. Have you tried using any of these?

best

Max

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAEa0ENq044N7ifOB29ov-N7r6YaNLny%2BWL3wsB%2B037X75NjwcQ%40mail.gmail.com.

Maximilian Haeussler

unread,

Jun 24, 2025, 8:15:16 AMJun 24

to Cohen Emiliano, Luis Nassar, UCSC Genome Browser Public Support

blat is very fast - per sequence. You can send it 100,000 sequences at a time. It just takes a long time to start up.

If you have small batches of 1-10 sequences at a time, then you're better off running a local gfServer and query it with "gfServer query" or gfClient. You will get the results faster than via our hgBlat.

On Tue, Jun 24, 2025 at 11:59 AM Cohen Emiliano <cohen.e...@mail.huji.ac.il> wrote:

Hi Luis and Max,

Thank you for responding, and for willing to help me.
Regarding running it locally - because of different reasons I have to work on a windows machine. There is a Linux machine that I can connect remotely through SSH, and I tried to run IsPcr (after I was blocked by the CAPTCHA) there but it was really slow when run against all the human genome (hg19.2bit, I need to make sure that the primers are specifics to the target region). Even after limiting it to fragments shorter than 2kbp.

I didn't know I could connect directly to your servers with gfClient - I will try it. Are there instructions? And what is gfPcr, can this tool allow me to run in silico PCR faster from my computer?

Sincerely,
Emiliano Cohen

Cohen Emiliano

unread,

Jun 24, 2025, 12:26:47 PMJun 24

to Maximilian Haeussler, Luis Nassar, UCSC Genome Browser Public Support

Hi Luis and Max,

Thank you for responding, and for willing to help me.

Regarding running it locally - because of different reasons I have to work on a windows machine. There is a Linux machine that I can connect remotely through SSH, and I tried to run IsPcr (after I was blocked by the CAPTCHA) there but it was really slow when run against all the human genome (hg19.2bit, I need to make sure that the primers are specifics to the target region). Even after limiting it to fragments shorter than 2kbp.

I didn't know I could connect directly to your servers with gfClient - I will try it. Are there instructions? And what is gfPcr, can this tool allow me to run in silico PCR faster from my computer?

Sincerely,

Emiliano Cohen

On Tue, Jun 24, 2025 at 12:27 PM Maximilian Haeussler <mhae...@ucsc.edu> wrote:

Gerardo Perez

unread,

Jun 30, 2025, 9:56:35 PMJun 30

to Cohen Emiliano, UCSC Genome Browser Public Support

Hello, Emiliano.

You can find details about both gfServer and gfClient on our BLAT Suite Program Specifications page:
https://genome.ucsc.edu/goldenPath/help/blatSpec.html

We also have additional resources that may be helpful when setting up BLAT servers for assembly hubs and running your own gfServer:

Adding BLAT servers for your hub: https://genomewiki.ucsc.edu/index.php/Assembly_Hubs#Adding_BLAT_servers
Running your own gfServer: https://genomewiki.ucsc.edu/index.php?title=Running_your_own_gfServer

We also have an FAQ entry for replicating web-based Blat percent identity and score calculations:
https://genome.ucsc.edu/FAQ/FAQblat.html#blat4

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAHhbv4pmA36LwVJbZjd-UXshR%3DzQT-%3D83mLcjxj3eGsBO8BHmg%40mail.gmail.com.

Reply all

Reply to author

Forward