software to convert pwm matrix to consensus sequence

Question

[pengchy]

Hi,

Is there a software or script to convert the position weighted matrix (PWM) into consensus sequences? I have searched the biostars and googled a while without any practical solution. Although there are many software derived consensus sequence from multiple alignment.

The PWM files were downloaded from CIS-BP (http://cisbp.ccbr.utoronto.ca/), but there is not consensus sequence along with the motif PWM file.

Best,

Pengcheng

Answer 1

[Zhilong Jia]

You can method to get consensus sequence by searching "m.consensus" in Biopython.

What is the definition of your mentioned consensus sequence? It seems that are some difference between that in WIki and in BioPython.

[pengchy]

Hi Zhilong,

Thank you for your reply. I have read the documentation of the biopython http://biopython-cn.readthedocs.org/en/latest/cn/chr14.html#id6.

Now I can read the PWM data into a dictionary class, Then how can I convert the dict class into Bio.motifs.matrix.PositionWeightMatrix class, through which the consensus can be derived using pwm.consensus method?

Thank you!

[pengchy]

Hi Zhilong,

I found the rsat convert-matrix can do the work. http://rsat01.biologie.ens.fr/rsat/. thank you!