Good Source For Dna Substitution Score Matrix / Matrices?

Question

[TabeaH]

Hi there,

I am looking for a place where I could find different DNA substution score matrices, such as .e.g. HOXD70 with information on the datasets they are based upon. Does any one of you maybe know a website or a similar source?

My alignments are currently based on HOXD70 (which is based on human and mouse sequences), but since my sequences are less diverged than mouse and human, I would like to have a more suitable matrix.

Thank you in advance for any ideas and answers!

[Michael]

Does this help to choose a model: http://en.wikipedia.org/wiki/Models_of_DNA_evolution#Most_common_models_of_DNA_evolution ?

Answer 1

[Charles Warden]

I've asked that same question myself. In my case, I wanted to just have a general idea about which amino acids substitutions were most common, so I used the matrix from one the original PAM papers.

This link contains both the matrix as a text file and a link to the corresponding paper:

http://cdwscience.blogspot.com/2012/06/combine-seattlesnp-and-gwas-catalog.html

Unfortunately, I don't have a more general answer to your question.

[Charles Warden]

Opps - I didn't read the question carefully. I agree that you should check out the wikipedia link

If you can find a copy at your local library, the situations for applying different matrices can be found in this book (which I think is a good introduction to molecular evolution):

http://www.amazon.com/Fundamentals-Molecular-Evolution-Dan-Graur/dp/0878932666

Answer 2

[odoluca]

Hello TabeaH, I was wondering if you managed to find any substitution matrix catalog.

I have short non-coding DNA motifs to be aligned and I am not sure which substiution matrix and gap penalties I should use. Any idea?

Cheers