Monday, January 22, 2007

Local Renyi

Additional material to submitted manuscript:
Local Rényi entropic profiles of DNA sequencesSusana Vingaa,b* and Jonas S. Almeidac,d
J. Theor. Biol. (submitted)
a Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID), R. Alves Redol 9, 1000-029 Lisboa, Portugalb Departamento de Bioestatística e Informática, Faculdade de Ciências Médicas – Universidade Nova de Lisboa (FCM/UNL), Campo dos Mártires da Pátria 130, 1169-056 Lisboa, Portugalc Dept Biostatistics and Applied Mathematics, Univ. Texas MDAnderson Cancer Center - unit 447, 1515 Holcombe Blvd, Houston TX 77030-4009, USAd Biomathematics Group, Instituto de Tecnologia Química e Biológica – Universidade Nova de Lisboa (ITQB/UNL), R. Qta. Grande 6, 2780-156 Oeiras, Portugal
E-mail addresses: svinga at algos inesc-id pt (SV), jalmeida at mdanderson org (JSA).
*Corresponding author

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DNA Datasets
Download text files (in FASTA format) with all the DNA sequences used in this study [].

Sequence name
Brief description
random with inserted motif L=3 'ATC'
random with inserted motif L=4 'ATCG'
random with inserted motif L=5 'ATCGA'
experimental promoter regions of B.subtilis - see paper for full description

MATLAB source code
Current version 1 (Jan. 19, 2007). Next upgrades will be posted here.
See an application example and look at functions' help. (NOTE: since these files were automatically generated some graphs appear differently from those in the manuscript).
Click to download all m-code MATLAB functions, which includes the following files:

File name
Brief description
Reads sequences from FASTA format files to struct MATLAB variables
Counts L-tuple repetitions for each position in input DNA sequences
Calculates probability density estimation matrix (KM) with fractal kernel. Calls kernel_analytical.m
Closed form for fractal kernel calculation
Normalizes KM estimations.
Finds the scale where maxima and minima of KM occur
Analyses specific user defined position/symbol
[Renyi continuous entropy][Alfréd Rényi's Biography][MATLAB site]
Suggestions &Comments: svinga at algos inesc-id ptCreated: 2007 Jan 19 -- Last update: 2007 Jan 19

Thursday, January 18, 2007

Fractal Density Kernel for Iterated Maps

A fractal density kernel for iterated maps of biological sequences was recently identified:

Almeida, J.S., S.Vinga (2006) Computing distribution of scale independent motifs in biological sequences. Algorithms for Molecular Biology. 1:18. [PMID:17049089].

The corresponding Matlab toolbox is available at