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DNA Forum Discuss DNA, the molecule of hereditary. Topics include DNA structure, DNA replication, DNA function.


highlighting sequence parts in a multiple alignment

highlighting sequence parts in a multiple alignment - DNA Forum

highlighting sequence parts in a multiple alignment - Discuss DNA, the molecule of hereditary. Topics include DNA structure, DNA replication, DNA function.


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Old 10-07-2011, 09:37 AM
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Default highlighting sequence parts in a multiple alignment



hey guys

I have the following problem: I aligned all available cDNA versions of a certain gene in clustalW or Mega5. It is obvious that different exons are spliced together to form similar domains in the final protein. I want to highlight this fact. Therefore I search for each exon and want to highlight it in the cDNA by a color code so I can see in which splice variant which part of the protein was combined by which exons. Unfortunately the alignment programs I use (Bioedit, MEGA5) don't allow to manually highlight sequences. If I export the file as rtf format I loose the alignment properties. If I export as a fasta I still have the alignment information but in text editor I cannot highlight with colors. I can export to excel, but there each nucleotide is in a single cell and I loose the ability to search for a certain exon sequence.

I hope somebody knows a program or an approach. Thanx
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Old 10-07-2011, 11:21 AM
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Default Re: highlighting sequence parts in a multiple alignment

afaik, genedoc with rtf. Its kinda old skool but serve your purpose I gather.
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