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Question for the wonderful science people...

P

Feel really dumb asking this, but: Please can any molecular people recommend programs or online tools for making multiple sequence alignments look pretty? I have a number of alignments (DNA and protein, some compare 2 sequences, some several) and I would like to add colours/shading to highlight similarities and differences. I can find a number or programs that will make each amino acid or nucleotide a particular colour, but that isn't what I'm after. Ideally, I would like a program that colours all the homologous regions green, all the rest red. Please can anyone help? It is purely an aesthetic thing for my thesis. Thank you.

H

I'm sure you could prolly do this with sybyl or one of it's add-ons, do you have that "kicking" around at uni?

P

Oooh, don't know that one. Ta H, I will try to find it. You rock!

H

If you have a computational chemistry or bioinformatics department, they will definately have it. I'm afraid to say it's not something you can just get hold of, Tripos charge a fortune for it!

A

The more interesting question is: who are the non-molecular people out there?

T

I agree with H. If all else fails you could do it manually...can clustalx be used? You can download that for free.

P

Thanks brajbio. I had the alignment I wanted using Clustal, but just wanted a programme to colour the areas of homology for aesthetics. I found a free, downloadable programme online called Genedoc which did exactly what I wanted - it is great and free and useful for little luddite me. Genedoc finds the residues that are conserved and also allows for motifs such as active sites to be highlighted in a different colour. It was all for making my thesis look pretty. Thanks again.

S

You should try BioEdit
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
It includes the ClustalW tool to make alignment
and you can customize the color.
Quite an intuitive program. I often use it.

P

Hi piglet while using genedoc for long seq..upto 2500 seq.it does not display first 500 seq. it comes in blue background why so? any idea?

W

Try GeneDoc - any colours you like! And idiot proof (even I can use it)...

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