Question

Represent Motifs On A Dna Sequence In A Graphical Way

9

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11.5 years ago

novino11 ▴ 90

I have few motifs whose location on a given DNA sequence has been identified using MATCH (from TRANSFAC). MATCH provides the location of these matrices in a numerical way as motif 1 236 (+) (for an example - motif 1 is present at location 236). I want to get a graphical output by feeding the length of DNA sequence and the the position of matrices so that its easy for presentation and comparing two different sequences with almost similar motifs

Thanks in advance for any suggestions

motif visualization • 4.8k views

ADD COMMENT • link updated 7.0 years ago by Biostar 20 • written 11.5 years ago by novino11 ▴ 90

score 6 · Accepted Answer · 2012-10-11

6

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11.5 years ago

Alex Reynolds 35k

Perhaps look at WebLogo, which assists with making sequence logos.

ADD COMMENT • link 11.5 years ago by Alex Reynolds 35k

score 5 · Accepted Answer · 2012-10-11

5

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11.5 years ago

Jeremy Leipzig 22k

You might want to look at berrylogo - it will be a more accurate means of visually comparing two motifs than a SeqLogo because a shift in nucleotide rank won't appear radically different

https://github.com/leipzig/berrylogo

ADD COMMENT • link 11.5 years ago by Jeremy Leipzig 22k

0

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Interesting tool!

ADD REPLY • link 11.5 years ago by Alex Reynolds 35k

score 3 · Accepted Answer · 2012-10-11

3

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11.5 years ago

Joseph Hughes ★ 3.0k

Have you tried the features and annotations options in Jalview

ADD COMMENT • link 11.5 years ago by Joseph Hughes ★ 3.0k

score 3 · Accepted Answer · 2012-10-11

3

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11.5 years ago

Mary 11k

I always liked Melina II for graphical display of the features on the sequence, and it gives a sequence logo as well. http://melina2.hgc.jp/public/index.html But if your motifs aren't identified with the selected tools they offer for "methods" I don't know if it would work for you.

ADD COMMENT • link 11.5 years ago by Mary 11k

score 2 · Accepted Answer · 2012-10-11

I think this depends on the length of your sequence. Our MSA editor can add comments to a sequence (manually or from a file), and then a "visual summary" can show 100s of kb in a single picture. The file format takes motif name, postion, strand, colour for showing these annotations on the sequence. You can then save this file locally (BBB is Java) http://athena.bioc.uvic.ca/virology-ca-tools/base-by-base/

Hillary, W., S.H. Lin, and C. Upton. 2011. Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments, BMC Microbial Informatics and Experimentation, 1:2

William Hillary, Song-Han Lin and Chris Upton*

Brodie, R., A.J. Smith, R.L. Roper, V. Tcherepanov, and C. Upton. 2004. Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments, BMC Bioinformatics, 5, 96.

Cheers, Chris