Annotating non-coding DNA (CRM): TF binding site analysis

Question

[Sarthok]

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.

Answer 1

[natasha.sernova]

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.