DNA motif search

[sikidiri]

Hello All,
I am wondering if there is any good DNA motif finding tool (having high sensitivity and specificity) for the non coding region or region out side the gene body.
Thanks in advance for your answer.

[hannat]

There is no perfect tool, if you have scored enhancers, then i would recommend you to use MDScan, if you have enhancers with no score distinction, then there are many which you can use Weeder, Meme, etc.

[sikidiri]

Thanks for your answer.
Problem with weeder is that I cann't submit more than 5 DNA sequences, with MEME also the problem is same. My data set is larger than this. Is there any DNA motif search tool which can look for motif/s in the downstream region?

[hannat]

for dna motif search, it is better to use short dna sequences as input, if you use large piece of dna as input, your motif search will not be as specific and as sensitive as you expected. So if you just use upstream few kb of lots of genes as input, i would say it is hard to get what you want, and even if you find programs to give you results, it will be hard for you to filter and choose the best suitable one. My suggestion is, if you have some motifs which you suspect might be functional, you can search them in your input, and compare to the background, to check weather it is enriched in your dna input.

[Livi81]

Are you analysing thousands of ChIP-Seq sites for example?
I really like 'Seqpos' that can be accessed within the nice biologist friendly interface of galaxy/cistrome under the 'Motif' tools. Otherwise 'Gadem' is another motif tool that can handle large datasets.

[frozenlyse]

I quite like gimmemotifs.

[KatherineMejiaGuerra]

MEME-ChIP

I found meme-chip like a good option.

Try the tutorialfor general use of the suite.

Currently MEME-ChIP (abstract) includes also DREME (abstract) and there is not limit for number of sequences.
...You provide MEME-ChIP with a set of sequences in FASTA format. Ideally the sequences are about 100 base-pairs long and enriched for motifs. The immediate regions around individual ChIP-seq "peaks" from a transcription factor (TF) ChIP-seq experiment are ideal. There is no limit on the number of sequences you provide, and they may be longer (or shorter) than 100 base-pairs if you desire. (The suggested 100 base-pair size is based on the typical resolution of ChIP-seq peaks.) We recommend that you "repeat mask" your sequences, replacing repeat regions to the "N" character... (Taken from MEME-ChIP tutorial)

Good luck!