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Subject: word occurence counting (DNA) From: ambrosia nightwish Date: 31 Mar, 2010 21:36:20 Message: 1 of 22 
Hello, 
"ambrosia nightwish" <mess_imen@yahoo.fr> wrote in message <hp0f8k$snf$1@fred.mathworks.com>... 
Subject: word occurence counting (DNA) From: ambrosia nightwish Date: 2 Apr, 2010 15:15:26 Message: 3 of 22 
I used FCGR toolbox to calculate the frequency of appearance of all the words with K length , I obtained a final matrix of frequencies.The purpose is to find the frequency of every word reads during the process of calculation. 
"ambrosia nightwish" <mess_imen@yahoo.fr> wrote in message <hp51me$adm$1@fred.mathworks.com>... 
Subject: word occurence counting (DNA) From: ambrosia nightwish Date: 2 Apr, 2010 15:45:43 Message: 5 of 22 
no not yet 
"ambrosia nightwish" <mess_imen@yahoo.fr> wrote in message <hp53f7$97n$1@fred.mathworks.com>... 
Subject: word occurence counting (DNA) From: ambrosia nightwish Date: 2 Apr, 2010 16:00:23 Message: 7 of 22 
in the FCGR toolbox of Jesús MenaChalco we have an example 
Subject: word occurence counting (DNA) From: ambrosia nightwish Date: 2 Apr, 2010 16:10:31 Message: 8 of 22 
if i have the sequence: AACCGTTAACGT, and i want to find the frequencies of all the dinucleotides (word of 2 letters for example), at the position 1 we read AA so the frequency of appearence is freq=1/12 , at the second position w read AC and freq=1/12, at the eighth position AA appeared fo the second time so freq=2/12 ,the calcul is stopped at the position Nlen+1 (N:length of the sequence, len: length of word) 
Subject: word occurence counting (DNA) From: Roger Stafford Date: 2 Apr, 2010 18:06:06 Message: 9 of 22 
"ambrosia nightwish" <mess_imen@yahoo.fr> wrote in message <hp54tn$2ii$1@fred.mathworks.com>... 
"ambrosia nightwish" <mess_imen@yahoo.fr> wrote in message <hp54tn$2ii$1@fred.mathworks.com>... 
Subject: word occurence counting (DNA) From: Ashish Uthama Date: 2 Apr, 2010 18:50:05 Message: 11 of 22 
On Fri, 02 Apr 2010 13:10:31 0300, ambrosia nightwish 
Subject: word occurence counting (DNA) From: ambrosia nightwish Date: 3 Apr, 2010 21:36:21 Message: 12 of 22 
THe problem still exists:The first solution shows the number of the counted words and gives a final result what I want to do is to find the number of appearance of words in every step i walk (increment by 1and word reading by wl), Let us take the same example s='AACCGTTAACGT' 
Subject: word occurence counting (DNA) From: Bruno Luong Date: 4 Apr, 2010 10:33:05 Message: 13 of 22 
Something like this? 
Subject: word occurence counting (DNA) From: ambrosia nightwish Date: 4 Apr, 2010 11:11:05 Message: 14 of 22 
That's working Bruno, thank you all 
Subject: word occurence counting (DNA) From: Bruno Luong Date: 4 Apr, 2010 13:38:05 Message: 15 of 22 
% Here is an vectorized code (not necessary meant faster) 
Subject: word occurence counting (DNA) From: ambrosia nightwish Date: 13 Apr, 2010 22:09:04 Message: 16 of 22 
"Bruno Luong" <b.luong@fogale.findmycountry> wrote in message <hp9pt1$go1$1@fred.mathworks.com>... 
"ambrosia nightwish" <mess_imen@yahoo.fr> wrote in message <hq2q20$aqn$1@fred.mathworks.com>... 
ambrosia nightwish wrote: 
Subject: word occurence counting (DNA) From: ambrosia nightwish Date: 14 Apr, 2010 00:25:08 Message: 19 of 22 
"Bruno Luong" <b.luong@fogale.findmycountry> wrote in message <hp9pt1$go1$1@fred.mathworks.com>... 
"ambrosia nightwish" <mess_imen@yahoo.fr> wrote in message <hq3213$eua$1@fred.mathworks.com>... 
Subject: word occurence counting (DNA) From: Bruno Luong Date: 14 Apr, 2010 08:15:22 Message: 21 of 22 
"ambrosia nightwish" <mess_imen@yahoo.fr> wrote in message <hq3213$eua$1@fred.mathworks.com>... 
Subject: word occurence counting (DNA) From: ambrosia nightwish Date: 15 Apr, 2010 15:20:25 Message: 22 of 22 
>The solution which I looked for was given by Bruno. Thank you all. 
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