Help with PScan and user defined matrices

Question

[naren.srinivasan]

Hi all,

First time poster here. I had a question regarding the program PScan.

I recently tried downloading all matrices from Jaspar and giving that list to Pscan (as I didn't want to limit myself to one model organism, PScan does). Unfortunately I received an error message :

Matrix with invalid name found! (only letters and digits allowed).Custom Matrices Error.

I was wondering if anyone had any advice on how to rectify these matrices to make them work in PScan ?

My current matrices look like this:

>MA0001.2    AGL3
A  [22 16 25 27  0  0 82 40 56 35 65 25 64  0 33 52 45 21 ]
C  [29  9  8 16 92 79  1  4  0  0  1  4  0  0 14  5 23 24 ]
G  [34 29  4 13  0  0  2  3  1  0  4  3 28 92 15  7 13 26 ]
T  [10 41 58 39  3 16 10 48 38 60 25 63  3  3 33 31 14 24 ]

Thanks!

Answer 1

[Ian]

According to the help page: http://159.149.160.51/pscan/help.html#Input you are very close:

>matrix1
A_1 A_2 ..... A_n
C_1 C_2 ..... C_n
G_1 G_2 ..... G_n
T_1 T_2 ..... T_n
>matrix2
A_1 A_2 ..... A_n
C_1 C_2 ..... C_n
G_1 G_2 ..... G_n
T_1 T_2 ..... T_n

You should be able to remove the A,C,T,G,[,], characters, you may have to remove the gene name too. Try it on a couple of matrices first.

E.g.

>MA0001.2
22 16 25 27  0  0 82 40 56 35 65 25 64  0 33 52 45 21
29  9  8 16 92 79  1  4  0  0  1  4  0  0 14  5 23 24
34 29  4 13  0  0  2  3  1  0  4  3 28 92 15  7 13 26
10 41 58 39  3 16 10 48 38 60 25 63  3  3 33 31 14 24

[naren.srinivasan]

Thanks!

Is there a way to do this en mass for all the transcription factors in the list without going through each one manually?