Question: Annotating non-coding DNA (CRM): TF binding site analysis
1
gravatar for Sarthok
3.1 years ago by
Sarthok70
Pennsylvania State University
Sarthok70 wrote:

Hello,

I am trying to annotate a ~300KB region from a insect genome which is a non-protein coding/ cis-regulatory region. I am primarily interested to identify all transcription factor binding sites. I have found lots of web based programs but not sure which one would be best fit for a insect genome?

I have also seen bioconductor packages to carry on transcription factor binding sites. If someone can point out to a comprehensive method to identify TF binding sites in a sequence that would be very helpful.

Thanks in advance for your help.

ADD COMMENTlink modified 3.1 years ago by natasha.sernova3.5k • written 3.1 years ago by Sarthok70
1
gravatar for natasha.sernova
3.1 years ago by
natasha.sernova3.5k
natasha.sernova3.5k wrote:

Try this site and use INSECT 2.0 - it is from 2016

http://bioinformatics.ibioba-mpsp-conicet.gov.ar/INSECT2/help.php

The first refence looks OK:

http://bioinformatics.oxfordjournals.org/content/32/8/1229.abstract

http://sci-hub.cc/ - to reach the whole text, use sci-hub.

although I would read all the information from the first site.

I am not sure it's the best program, but it's one of the latest ones.

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by natasha.sernova3.5k
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