coloring motifs

[Minou Bina]

Hello

I have a list of motifs that I would like to display in different colors in the same track along chromosomes.
Would you please info about how it could be done. Thank you

Minou Bina
Purdue University

[Jonathan Casper]

Hello Minou,

Thank you for your question about displaying motifs in different colors in a browser track. When you say that you have motifs, do you mean that you have a set of chromosome positions that correspond to your motifs? If so, you can turn those positions into a BED track with RGB color information to display each motif in a color of your choice. The format for a BED track with color is described at http://genome.ucsc.edu/FAQ/FAQformat.html#format1. Note particularly the second of the three examples, which shows using the RGB color field. If you do not have positions, and instead just have a set of motif sequences, then you will need to align your motifs to a genome assembly before you can display them. Unless you have long motifs (over 25 bases), BLAT will probably not be able to handle the alignments for you. You may have more success with a short read alignment tool like Bowtie. After you obtain the alignment results, then you should be able to construct a BED track as described above.

You may also be interested in our oligoMatch tool, which specifically searches for perfect sequences matches. More information about oligoMatch can be found in the answer to this mailing list question: https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/LgyVIcTONpk/discussion.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

Minou Bina
Purdue University

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