Sequences as pictures

The supporting m-files for manuscript in press (BMC Bioinformatics)

Biological sequences as pictures – a generic two dimensional solution for iterated maps

Jonas S Almeida1*, Susana Vinga2

1) Dept Bioinformatics and Computational Biology, University of Texas MDAnderson Cancer Center, Houston, Texas, USA. Email: jalmeida@mdanderson.org.
2) Knowledge Discovery and Bioinformatics, Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento, Lisboa, Portugal. Email: svinga@kdbio.inesc-id.pt.

are provided here.

The command that starts the GUI depicted in Figure 1 is "nCGR".

The command to calculate the map increment (Equation 2) is "salto". The same commend for the preceeding solution (equation 1) is "salto_fiser". To reproduce the plots in the reamining figures you can generate random sequences using "uni_randa" and the use "n_gon_plt" :

>> help n_gon_plt
N_GON_PLT plots n-gon assembled by CREATE_DT
alternatively the string may be submitted directly
in which case a seccond optional input argument can be used to specify
the increment
Syntax: function y=n_gon_plt(dt,inc)

Examples

a) submit sequence
n_gon_plt('qwerqerqewrqerqrqewrqwerqwerqwrqwerqwerqrqewrqeerwretrwertwtwrw
rtrtwr');

b) build structure first
str='qwerqerqewrqerqrqewrqwerqwerqwrqwerqwerqrqewrqeerwretrwertwtwrwrtrtwr';
dt1=create_dt(str);
dt2=create_dt(str,0.7);
figure;subplot(1,2,1);n_gon_plt(dt1);subplot(1,2,2);n_gon_plt(dt2);

Jonas Almeida, Jan 2009, jalmeida@mdanderson.org