Scan Fasta file in Jaspar but says 'longer than 20000 nucleotides'.

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10.4 years ago

muhe1985 ▴ 20

Hello!

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

ChIP-Seq sequencing alignment • 2.8k views

ADD COMMENT • link updated 2.9 years ago by Ram 44k • written 10.4 years ago by muhe1985 ▴ 20

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

ADD REPLY • link 10.4 years ago by Neilfws 49k

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

ADD REPLY • link 10.4 years ago by muhe1985 ▴ 20

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

ADD REPLY • link updated 5.1 years ago by Ram 44k • written 10.4 years ago by Neilfws 49k

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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 REPLY • link updated 2.9 years ago by Ram 44k • written 10.3 years ago by Chris Evelo 10k

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