SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GO term clustering cgault General 1 10-28-2013 09:43 PM
clustering RNASeq data PFS Bioinformatics 0 06-21-2011 10:14 AM
AVA clustering Xterra 454 Pyrosequencing 0 12-04-2010 06:51 AM
Clustering gene expression pattern of next generation seq data zhlyang Bioinformatics 0 12-02-2009 03:03 PM

Reply
 
Thread Tools
Old 07-17-2009, 01:19 AM   #1
asankaf
Member
 
Location: clayton

Join Date: Jan 2009
Posts: 10
Default gene clustering using motif

Hi,

I am new to molecular biology and I am going to cluster yeast gene using several data sources. I know that gene can be clustered using gene expression data and using other alternatives. I klnow that motif frequencies is also a nother solution. I have read in a paper that using frequency measure of motifs we can cluster genes. how can i use motif to cluster genes.
Can anyone tell me how to find motif frequencies for a geven gene.
for ex: how to find frequency motif for gene STU2 (from yeast genome)

Thanks a lot in advance,
Asanka.
asankaf is offline   Reply With Quote
Old 07-17-2009, 04:24 AM   #2
ljxue
Junior Member
 
Location: China

Join Date: Jul 2009
Posts: 4
Default

Firstly, a list of motifs should be obtained from some databases containing transcription factor binding site. Or you can get the motifs from your data using tools such as MEME,
Then map the elements onto your sequences using Patscan and so on.
Then summarize the number of sites.
ljxue is offline   Reply With Quote
Old 07-17-2009, 07:53 PM   #3
asankaf
Member
 
Location: clayton

Join Date: Jan 2009
Posts: 10
Default

thanks a lot for your suggestions.
here I only know the gene name. how can I find a sequence for a given gene.
to find motif ,what sequence we use? DNA(in terms of A,T,C,G) or PROTIEN?
asankaf is offline   Reply With Quote
Old 07-17-2009, 09:58 PM   #4
ljxue
Junior Member
 
Location: China

Join Date: Jul 2009
Posts: 4
Default

I do not work on yeast, you can try the page
http://www.yeastgenome.org/cgi-bin/seqTools

Mostly,regulatin motifs refers to the cis-elements of the gene promoters.
The method I said it not for green hand.You can ask others good at
bioinformatics to help you to deal with your data.

If you want to cluster genes using the seqences of CDS,cDNA, or protein
you can simplely use MEGA. Your can also find these sequences
in http://www.yeastgenome.org

Last edited by ljxue; 07-17-2009 at 10:12 PM.
ljxue is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:22 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO