Help in genome browser to search and annotate a particular sequence

[PANKAJ GUPTA]

Hello ,

I am a PhD student from Indian Institute of Technology Kanpur INDIA,

I am wondering is there any way by which I can search a particular 6bp sequence (ex: CGGCGG) in genome and annotate it by some name and label with some method so that when I see in genome browser I can visualize that region like by peak or color anything. 

 

It is important because I want to search this sequence in -10kb region of my favorite gene and if it present I want to locate 1.5kb sequence around this sequence and know about other Transcription Factor Binding Site in this -1.5kb region.

If there is any way to do please let me know. 

Waiting for response.Thanks in advance

-- 

Pankaj Gupta
C/o Dr.Amitabha Bandyopadhyay
Developmental Biology lab [Lab # 10]
Department of Biological Science and Bioengineering (BSBE)
Indian Institute of Technology
Kanpur
Uttar Pradesh. 
India
208016
Mob.No. 09756601175
Ph.No-  512-259-4057 

[Christopher Lee]

Hi Pankaj,

Thank you for your question about searching for short sequences. If
you just want a simple visual cue of where the sequence you are
interested in is, you can use the "Short Match" track to find all
matches to a short sequence. Navigate to your gene of interest and
then click on the "Short Match" track in the Mapping and Sequencing
group and enter your short sequence into the text box to find all
matches.

If you would like a BED file of these matches, you can use the
findMotif utility. Please see this previously answered mailing list
question for more information:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/zlvaV8Wzeaw/YJ-rRv7FPRQJ

In short, download the appropriate findMotif utility for your system
from http://hgdownload.soe.ucsc.edu/admin/exe/, then download the 2bit
file for the genome you are interested in, and then run findMotif on
the short sequence you are interested in:
findMotif -motif=CGGCGG hg38.2bit

For a full list of options on how to use the findMotif utility, run it
with no arguments:
findMotif

Once you have this BED file, you can upload it as a custom track and
then use the Genome Browser as you propose, searching for a gene,
navigating downstream and grabbing flanking sequence if your motif
(visualized in the custom track) is present.

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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