For
all programs in C, key in the command without any input arguments and a help
message will be displayed. For example, if you do not know how to use
GetSignal, just key ‘GetSignal’ at the command prompt and you will get a
message on how to use GetSignal.
For
all matlab functions, key in ‘help <function>’ and a message about the
function will be displayed. For example, if you want to get help for
ExtractGetSignal, just key in ‘help ExtractGetSignal’ at the Matlab command prompt
and a help message will be displayed.
- GetSignal (C)
- Description: Converts all sequences in <input fasta file> to
signals (raw signals, windowed signals, wavelet reconstructed signals)
with all indices listed in <input index file>
- Usage: GetSignal <input fasta
file> <input index file> <signal file> <window file>
<wave file> <WIN> <LEVEL> <type(a/d)>
- (input)
Input fast file = your sequences in fasta format
- (input)
Input index file = list of aa indices that you want use (using their
AAIndex) (for the format, refer to aaid_489.out)
- (output)
signal file = raw signals translated from sequences using aa indices
- (output)
window file = WIN length window-averaged signal obtained from raw signal
(If WIN=1, then the windowed signal is the same as raw signal)
- (output)
wave file = reconstructed wavelet signal determined by LEVEL and type
(a/d). In this program, ‘db10’ wavelets are used.
- (parameter)
WIN = Rectangular window size
- (parameter)
LEVEL = wavelet level
- (parameter)
type (a/d) = Approximation (a) or detailed (d)
- Example: GetSignal kinase.fasta aaid_489.out kinase_sig
kinase_win kinase_wave 1 2 a
- This
command will give you 3 output files : kinase_sig, kinase_win and
kinase_wave
- The
wave file contains the the reconstructed signal obtained from level 2
approximation wavelet transformation using wavelet ‘db10’
- Output file format:
- The
first line contains 2 integers: <no of sequences>N <no of aa indices> M
- Subsequent
lines contain the information for each seqence. If you have N sequences
in your input fasta file, then you will have N+1 lines in your output
files.
- From
2nd line onwards, each line contains the information of a
single sequence:
- First
value is an integer which tells you the length of the sequence, L
- Subsequencly,
there are M x L sets of float values which represents the signal for
sig. Not that if WIN is not 1, then there will be M x (L-WIN+1) sets of
values for win and wave file.
- To
load the values into MATLAB,
use ExtractGetSignal.m
- ExtractGetSignal.m
- Description: Read signal generated by a C program
GetSignal
- Usage:
[sig,sig_len]=ExtractGetSignal(filename)
- (Input)
Filename = The signal filename generated by GetSignal (kinase_sig,
kinase_win and kinase_wave)
- (output)
sig = values of the signals; N x M x max(L) array where N is the number
of sequences, M is the number of indices and L is the length of the
signal.
- (output)
sig_len = length of each sequence; N x 1 array where N is the number of
sequences since sequences may be of different length.
- Example:
[kinase_sig,kinase_len]=ExtractGetSignal(‘kinase_sig’)
- This
will give you a N x M X max(L) array for kinase_sig and Nx1 array for
kinase_len
- To
plot the signals, use plotwave.m
- Plotwave.m
- Description: plot 2D signals for 3D arrays. The
plot function in MATLAB cannot handle 3D data, that is it can’t do plot(kinase_sig(1,1,:))
- Usage:
plotwave(seq_choice,index_choice,seq_wave,holdgraph,color)
- Seq_choice
= which sequence you want to plot
- Index_choice
= which index you want to plot (Note that in this case, you have to know
the order of the indices in your <input index file>.
- Seq_wave
= the variable that holds the 3D data
- Holdgraph
= a flag that tells the plotwave function if you want to overlay the
graph or start a new figure (1 = overlay, 0 = start a new figure)
- Color
= color of the graph you want to plot
- Example: plotwave(1,1,kinase_sig,1,’r’)
- A
graph of the first sequence of kinase_sig converted with the first aa
index listed in the <input index file> is plotted in red line
- GetSignalOneStop.m
- Description:
- Get all AA indices wanted from 'aa_filename', store accession
into aa_id and values into norm_aa_index.
- Read in sequences from 'fasta_filename' and store in
seq_name, seq and seq_len.
- Obtain raw signal with all the AA indices
- Perform windowing with size 'win' and store in sig_win
- Perform wavelet transformation and store in wave
- The coefficients stored in wave is based on 'level' and
'choice'.
- Usage:
[aa_id,norm_aa_index,seq_name,seq,seq_len,signal,sig_win,wave]=GetSignalOneStop(aa_filename,fasta_filename,win,level,choice,wavelet)
- GetRawSignal.m
- Description:
- Read
in wanted indices from 'aa_filename' and store accession into aa_id and
values of these indices into norm_aa_index
- Read
raw sequences read from 'fasta_filename' and store into seq_name, seq,
seq_len
- Convert
sequences to raw signals using these indices and store in signal
- Usage:
[aa_id,norm_aa_index,seq_name,seq,seq_len,signal]=GetRawSignal(aa_filename,fasta_filename)
- EuclideanDistance.m
- Description: Return a single value for euclidean
distance between x and y
- Usage: [dist]=EuclideanDistance(x,y)
Download C Sourcecode
Download Matlab files