Question: Scan Fasta file in Jaspar but says 'longer than 20000 nucleotides'.
gravatar for muhe1985
5.7 years ago by
United States
muhe198520 wrote:


I am new here.

I just get the fasta sequence from a published BED file using UCSC genome browser.

Now I want to scan a potential transcription factor binding site using Jaspar. However, on the Jaspar website it returns 'You are submitting a sequence longer than 20000 nucleotides. This is beyond the scope of the database. Try out ConSite'

And the link to 'Consite' is not active


Anyone knows how to work around with this issue? I assume scanning large fasta files converted from ChIP-Seq is a common practice



sequencing chip-seq alignment • 1.4k views
ADD COMMENTlink modified 5.5 years ago by Biostar ♦♦ 20 • written 5.7 years ago by muhe198520

Usual solution to restrictions at the website is to download and install the software locally.

ADD REPLYlink written 5.7 years ago by Neilfws48k

Thank you!! I am new to bioinformatics, I just googled and did not find that the Jaspar offer desktop version

ADD REPLYlink written 5.7 years ago by muhe198520

Try their download link; you should also look at the MEME suite, which can be used with the JASPAR databases.

ADD REPLYlink modified 4 months ago by RamRS25k • written 5.7 years ago by Neilfws48k

In cases like this, where part of a service doesn't work, please use the contact options given and inform the people running the service. Running complex services is hard and people really don't always know when they are partly broken. 

ADD REPLYlink written 5.5 years ago by Chris Evelo10.0k
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