Please fix this code

protein1=input('Please input GenPept code of the first protein: ', 's');
protein2=input('Please input GenPept code of the second protein: ', 's');

disp('Please wait, this can take a while')
for step = 1:50
    fprintf('.')
end

seq1 = getgenpept('protein1','SequenceOnly',true);
seq2 = getgenpept('protein2','SequenceOnly',true);

When I input AAA69808 for protein 1, it gives error

[Image Analyst]

You forgot to post the error message ( all the red text , not just part of it.)

[Geoff Hayes]

Ahmad - if the code is returning an error of some kind, then please copy and paste the full error message to your question. Of particular interest is the line number that generated the error.

[Ahmad]

well it's no longer giving error!!! this is weird, I think it had to do with previous running code, is there a way to terminate all processes on MATLAB?!

btw, if i want the dots to appear more slowly in the for loop, what do I do?!

it didn't work btw

Please input GenPept code of the first protein: AAA69808
Please input GenPept code of the second protein: NP_989750
Please wait, this can take a while
..................................................Warning: The record protein1 has been replaced by NP_001069837

!!!

Answer 1

[Image Analyst]

Here's some code you can run to clean things up at the beginning of a script.

clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
clear;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.

Try putting that into a quick launch toolbar button called "Clean up" for easy single-click running of it.

[Ahmad]

thx plz help me i continue to get this error! look at this example here:

http://www.mathworks.com/help/bioinfo/examples/using-scoring-matrices-to-measure-evolutionary-distance.html

I'm trying to take those NCBI reference codes as input from the user, this is what i wrote:

protein1=input('NCBI reference sequence of the first protein: ', 's');
protein2=input('NCBI reference sequence of the second protein: ', 's');

disp('Please wait, this can take a while')
for step = 1:100
    fprintf('.')
end

seq1 = getgenpept('protein1','SequenceOnly',true);
seq2 = getgenpept('protein2','SequenceOnly',true);

but I get this "warning"

Warning: The record protein1 has been replaced by NP_001069837.
Returning record 115496762 
> In bioinfo\private\getncbidata>accession2gi at 425
  In bioinfo\private\getncbidata at 189
  In getgenpept at 67
  In Untitled at 14 
Warning: The record protein2 has been replaced by NP_001098798.
Returning record 157427784 
> In bioinfo\private\getncbidata>accession2gi at 425
  In bioinfo\private\getncbidata at 189
  In getgenpept at 67
  In Untitled at 15

[Image Analyst]

Ahmad, I formatted this post for you but for the future, read this.

Sorry I can't answer because I don't have the Bioinformatics Toolbox and I don't know what those functions do.

Answer 2

[Luuk van Oosten]

I believe the warning is of no importance to you. Note the difference between different protein annotations, I think that is what is confusing you. It seems that accession numbers are converted to GI nrs.

Have a look here

sequence IDs

And here

accession nrs