This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Search for a "standard" PWM for Kozak Sequence

Hello,

I am looking for a "standard" PWM for the Kozak sequecne in humans. I have searched through many papers, but they tend to leave out the actual matrix that they generate/use.

Thanks

Edit: I found the original Kozak paper which has a PWM, but I am still wondering if there is a more recent one.

genome motif kozak
• 3,419 views • link
updated by Ram Ram • written by mbio.kyle mbio.kyle

1 answer

could you please share the PWM? Thanks!

• 0 views • link
written by Ming Tommy Tang Ming Tommy Tang

Hey! Sorry this was from a while ago so I don't have the paper. I do have the matrix though. Each row is a position, I THINK it was in the order ACGT (alphabetical) so I added those labels but I would find the original paper and double check (This matches the ATG so it is probably right). I think if a position was less than one we just set it too zero.

A  C  G  T
25 53 15 07
61 02 36 01
27 49 13 11
15 55 21 09
97 00 00 00
00 00 00 97
00 00 97 00
23 16 46 15
• 0 views • link
updated by Ram Ram • written by mbio.kyle mbio.kyle

Thanks for sharing, and I would like to see the paper as well:)

• 0 views • link
written by Ming Tommy Tang Ming Tommy Tang

I can see if I have it at work tomorrow or later this week.

• 0 views • link
written by mbio.kyle mbio.kyle

Log in to answer this question.

More posts like this