Question: RNA binding motif
0
gravatar for Aishwarya Kulkarni
4.2 years ago by
United States
Aishwarya Kulkarni60 wrote:

I am doing an RNA binding motif scan on exons and I am using the bed files provided by ENSEMBL for scanning the exonic positions which are traced back to the genomic positions. My question is that , if I the binding consensus sequence for the RBP is GCTT then on the negative stranded position would we want to scan for the GCTT binding position or AAGC binding position.

rna rbp • 1.6k views
ADD COMMENTlink modified 4.2 years ago by Devon Ryan89k • written 4.2 years ago by Aishwarya Kulkarni60
4
gravatar for Devon Ryan
4.2 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

You'll look for the AAGC to catch binding on the other strand. BTW, you might just scan the transcriptome, since then everything will be on the same strand.

ADD COMMENTlink written 4.2 years ago by Devon Ryan89k

Thanks, also since I am new to this area where can I find the whole transcriptome to download and using for scanning?

ADD REPLYlink written 4.2 years ago by Aishwarya Kulkarni60

In UCSC you can use the 'Table Browser' and in Ensembl the 'BioMart'

ADD REPLYlink written 4.2 years ago by David Langenberger8.7k

FTP is faster :)
 

ADD REPLYlink written 4.2 years ago by Devon Ryan89k

It is, but for beginners the browser versions might be more convenient. :)

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by David Langenberger8.7k

From UCSC, it's the transcriptome.fa.gz file available on their FTP servers. For Ensembl it's under the cDNA directory (e.g., here's the directory for humans).

ADD REPLYlink written 4.2 years ago by Devon Ryan89k
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