Finding Common Motifs In Sequences
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Entering edit mode
12.2 years ago
Fabio ▴ 120

I have a few hundred yeast sequences (20-80bp long) and I want to find common motifs (conserved bases at certain indices) in them. I am using a Mac

motif • 19k views
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9
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11.7 years ago
Stew ★ 1.4k

I would recommend MEME as others, however Weeder is also very easy to install and run on a Mac. It is word based and runs a lot faster than Meme, with a far fewer options.

If you would like something to run specifically on your Mac you could try iMotifs, which incorporates the NestedMICA algorithm for discovering over-represented motifs.

For a small set of sequences, such as yours, you could also use Meme, Weeder or others online without installing them locally. Finally, the Regulatory Sequence Analysis Tools (RSAT) ( http://rsat.ulb.ac.be/rsat/ or http://rsat.ccb.sickkids.ca/) are a great place to start for pattern matching and discovery.

In case it is of any use I have put up a short presentation about DNA motif finding from a course I gave earlier this year. You can find it here.

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12.2 years ago
Tom Koerber ▴ 60

You can also use MEME: http://meme.sdsc.edu/.

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11.8 years ago

Some time ago I used SOMBRERO (http://bioinf.nuigalway.ie/sombrero/download.html) with a good degree of success on finding motifs in a very diverse set of sequences. They have a Mac version for download as well as parallel versions for Irix and Linux.

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5
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11.8 years ago

The first step when looking for conservation of single bases or motives is often a multiple sequence alignment that will align the sequences in a way such that conserved regions are best visible. This can be a first step before using explicit motif finders like MEME. A good way of visualizing multiple alignments is the sequence-logo that will give a graphical representation of base conservation.

Here is the wikipedia list of mult.-sequence alignment tools.

I recommend to start with the EBI web-server of ClustalW though, if that is not enough you can also try MAFFT or T-Coffee.

Weblogo can generate sequence-logo graphics from the output and also from fasta input directly.

Advantage of these tools is that you don't need to install them, so good for a first attempt irrespective of using a Mac.

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4
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11.9 years ago

Meme has been the first program to be published for doing that. As an alternative you can find one of the EMBOSS tools; if you are scared by a terminal and want to do it from a web-based interface, you can use the EMBOSS tools from galaxy

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11.8 years ago
Darked89 4.2k

You may check out these pages:

These are ca 2 years old (links may not work etc.) but as a starting point should be OK. Also in unlikely case you did not found it yet: in yeast there has been an extensive motif search study done by Kellis with insane number of citations:

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12.2 years ago
Zhenhai Zhang ▴ 170

try this out?

http://fraenkel.mit.edu/webmotifs/form.html

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12.2 years ago
Suk211 ★ 1.1k
ACGGGCCCGACGATGCGTCGTA
ACGTACGTCGAACCGTCGTCGT
ACGTGCGTCGAAACGTCAGTCG
ACGGGTTCGATCGTCGTCGTCG

may be in Python I will break down the first sequence of required motif length into a sliding window and will search for those list of motifs in the rest of sequences using regular expression in python using re.search() method.

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post the python code as well (put it into pre tags then it will be shown nicely formatted, see help on the right)

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8.0 years ago
sanchezcavani ▴ 220

I would recommend to use MEME.

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