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Xugang Ye

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National Center for Biotech Info. / Johns Hopkins University

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Applied mathematician and machine learning specialist


 

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05 Dec 2011 Screenshot Find an ungapped pattern window from a set of protein sequences This program is to find an ungapped pattern window of certain width from a set of protein sequences Author: Xugang Ye bioinformatics, machine learning, dirichlet mixture mod..., pattern search, protein sequences, pattern 11 15
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06 Dec 2011 Find an ungapped pattern window from a set of protein sequences This program is to find an ungapped pattern window of certain width from a set of protein sequences Author: Xugang Ye

Dear Professor Prandtl,

I used a 20-component Dirichlet mixture prior that is provided by UCSC, here is the website:

http://compbio.soe.ucsc.edu/dirichlets/index.html

The prior as defult in this program is called "recode4.20comp". But the order of the amino acid letter is different, they use "ACDEFGHIKLMNPQRSTVWY", but I use "ARNDCQEGHILKMFPSTWYV". Make sure the prior and the order of letters are consistent.

Xugang

05 Dec 2011 Find an ungapped pattern window from a set of protein sequences This program is to find an ungapped pattern window of certain width from a set of protein sequences Author: Xugang Ye

Hi, Judy,

Yes. By the way, Could you let me know what Lab are you working for? Thanks.

Xugang

05 Dec 2011 Find an ungapped pattern window from a set of protein sequences This program is to find an ungapped pattern window of certain width from a set of protein sequences Author: Xugang Ye

Hi, Judy,

Thanks for your interest of using the codes. First, upload the folder to your server if you have not done so. Then enter the sub-folder codes. And the .c file you mentioned is find_patternwindow_v4_1.c
that's a computing function written in c language. Other than directly using the usual gcc compiler, you need to use mex to compile it so that the function can be called by your matlab scripts.
type "mex -setup", then you may be given several options. In linux/unix I recommanded, you just chose the first option that use gcc-mex compiler. When you are asked whether to overwrite the file mexopts.sh, you answer is yes. Then the next is simply to type

mex find_patternwindow_v4_1.c

you will find that an executable file

find_patternwindow_v4_1.mexa64

is created. Then you have matlab function
find_patternwindow_v4_1() to use.

Feel free to ask any question

Xugang

05 Dec 2011 Find an ungapped pattern window from a set of protein sequences This program is to find an ungapped pattern window of certain width from a set of protein sequences Author: Xugang Ye

Fantastic work! I am a researcher at the National Institutes of Health, Bethesda, MD, I found this program is very useful to my research in sequence-based domain detection.

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08 Jan 2013 Find an ungapped pattern window from a set of protein sequences This program is to find an ungapped pattern window of certain width from a set of protein sequences Author: Xugang Ye Tammy Tatley

It's very useful for my research at Fox Chase Cancer Center! I hope more people in this field will know this to help their research.

16 Dec 2011 Find an ungapped pattern window from a set of protein sequences This program is to find an ungapped pattern window of certain width from a set of protein sequences Author: Xugang Ye Ying

16 Dec 2011 Find an ungapped pattern window from a set of protein sequences This program is to find an ungapped pattern window of certain width from a set of protein sequences Author: Xugang Ye Prandtl

15 Dec 2011 Find an ungapped pattern window from a set of protein sequences This program is to find an ungapped pattern window of certain width from a set of protein sequences Author: Xugang Ye Ying

15 Dec 2011 Find an ungapped pattern window from a set of protein sequences This program is to find an ungapped pattern window of certain width from a set of protein sequences Author: Xugang Ye Ying

Very useful code. Thanks a lot!

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