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Analysis of single-strand exceptional word symmetry in the human genome: new measures

V. Afreixo, J. M. O. S. Rodrigues, C. A. C. Bastos
2014 Biostatistics  
We conclude that the global symmetry present in the human genome is clearly exceptional and significant. The chromosomes present distinct exceptional symmetry profiles.  ...  There are several exceptional word groups and exceptional words with a strong exceptional symmetry.  ...  We showed the exceptional symmetry profiles using 12 different word lengths.  ... 
doi:10.1093/biostatistics/kxu041 pmid:25190514 fatcat:sjivp4fxv5az3a2w6nowuzihdy

The exceptional genomic word symmetry along DNA sequences

Vera Afreixo, João M. O. S. Rodrigues, Carlos A. C. Bastos, Raquel M. Silva
2016 BMC Bioinformatics  
Results: To explore the exceptional genomic word symmetry along the genome sequences, we propose a sliding window method to extract the values of exceptional symmetry (for all words or by word groups).  ...  We compare the exceptional symmetry effect size distribution in all human chromosomes against control scenarios (positive and negative controls), testing the differences and performing a residual analysis  ...  Ciência e a Tecnologia"), within projects: COMPETE/FEDER UID/BIM/04501/2013 and PEst-OE/EEI/UI0127/2014.  ... 
doi:10.1186/s12859-016-0905-0 pmid:26842742 pmcid:PMC4738807 fatcat:a2h7ym75lndvhp6pci2ina2n7q

Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities

Vera Afreixo, João M O S Rodrigues, Carlos A C Bastos
2014 Journal of Integrative Bioinformatics  
We created a new organism genomic signature consisting of a vector of the measures of exceptional symmetry for words of lengths 1 through 12.  ...  In this work, we measure the symmetry above that expected in independence contexts (exceptional symmetry), for several organisms: viruses; archaea; bacteria; eukaryotes.  ...  Leveraging on this measure,we created a kind of organism genomic signature which is an exceptional symmetry profile (the vector with the first 12 measures of exceptional symmetry).  ... 
doi:10.2390/biecoll-jib-2014-250 pmid:25339084 fatcat:zidu7fi52jazzakxmykeopn4eq

Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities

Vera Afreixo, João M. O. S. Rodrigues, Carlos A. C. Bastos
2014 Journal of Integrative Bioinformatics  
We created a new organism genomic signature consisting of a vector of the measures of exceptional symmetry for words of lengths 1 through 12.  ...  In this work, we measure the symmetry above that expected in independence contexts (exceptional symmetry), for several organisms: viruses; archaea; bacteria; eukaryotes.  ...  Leveraging on this measure,we created a kind of organism genomic signature which is an exceptional symmetry profile (the vector with the first 12 measures of exceptional symmetry).  ... 
doi:10.1515/jib-2014-250 fatcat:7uhsduchvza7tgcbafmzqlx4ie

Two common profiles exist for genomic oligonucleotide frequencies

Shang-Hong Zhang, Lei Wang
2012 BMC Research Notes  
It was reported that there is a majority profile for trinucleotide frequencies among genomes.  ...  Conclusions: The causes for the existence of two common profiles would mainly be GC content variations and strand symmetry of genomic sequences.  ...  Genomes without either sufficiently low (high) GC content or a sufficiently high level of strand symmetry could not produce a common profile.  ... 
doi:10.1186/1756-0500-5-639 pmid:23158698 pmcid:PMC3532236 fatcat:4ju7obb7jvdkjg3cqdlsrl326q

On the comparison of regulatory sequences with multiple resolution Entropic Profiles

Matteo Comin, Morris Antonello
2016 BMC Bioinformatics  
The Entropic Profile is a function of the genomic location that captures the importance of that region with respect to the whole genome.  ...  As a byproduct we provide a formula to compute the exact variance of variable length word counts, a result that can be of general interest also in other applications.  ...  The Entropic Profiler takes a genome in input and evaluates a function of the genomic location that captures the importance of that region with respect to the whole genome.  ... 
doi:10.1186/s12859-016-0980-2 pmid:26987840 pmcid:PMC4797186 fatcat:ixavuwdp5rdk7jqlqtfxadredq

Local Renyi entropic profiles of DNA sequences

Susana Vinga, Jonas S Almeida
2007 BMC Bioinformatics  
, overlapping scales, with significant future applications in the recognition of foreign genomic material and inference of motif structures.  ...  Subsequent work proposed a fractal pdf kernel as a more exact solution for the iterated map representation.  ...  Sophie Schbath (INRA, France) for her comprehensive explanation of the statistical properties of Chi sequences and for kindly providing the processed genomes used in her previous analysis.  ... 
doi:10.1186/1471-2105-8-393 pmid:17939871 pmcid:PMC2238722 fatcat:ffadas4h2jgs7lc5tq6e4cgxz4

Hereditary profiles of disorderly transcription?

Johannes W I M Simons
2006 Biology Direct  
Moreover such a specific deviating profile appeared to be epigenetic in origin and could be stably transmitted to a clonal derivative e.g. from a precancerous normal tissue to its tumor.  ...  The aim of this study was to establish whether a disorderly state could occur that adversely affects gene expression profiles and whether such a state might have biomedical consequences.  ...  The availability of the Cancer Genome Anatomy Project's (CGAP) SAGE (Serial Analysis of Gene Expression) database of human gene expression levels in a wide variety of cells [11] has enabled us to check  ... 
doi:10.1186/1745-6150-1-9 pmid:16579860 pmcid:PMC1500996 fatcat:f3fpzp2ornhxplwnasrvr3ktnu

Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics

Siamak Ravanbakhsh, Philip Liu, Trent C. Bjordahl, Rupasri Mandal, Jason R. Grant, Michael Wilson, Roman Eisner, Igor Sinelnikov, Xiaoyu Hu, Claudio Luchinat, Russell Greiner, David S. Wishart (+1 others)
2015 PLoS ONE  
profile.  ...  This paper presents a tool, Bayesil, that can quickly, accurately and autonomously produce a complex biofluid's (e.g., serum or CSF) metabolic profile from a 1D1H NMR spectrum.  ...  In other words, metabolomics is not yet automated.  ... 
doi:10.1371/journal.pone.0124219 pmid:26017271 pmcid:PMC4446368 fatcat:x6nmy7l4ofhavnqig4vgqx6wj4

Concurrent Whole-Genome Haplotyping and Copy-Number Profiling of Single Cells

Masoud Zamani Esteki, Eftychia Dimitriadou, Ligia Mateiu, Cindy Melotte, Niels Van der Aa, Parveen Kumar, Rakhi Das, Koen Theunis, Jiqiu Cheng, Eric Legius, Yves Moreau, Sophie Debrock (+6 others)
2015 American Journal of Human Genetics  
A. Destouni for critical reading of the manuscript.  ...  (E and F) The genome-wide haplarithm profiles of the same samples derived from continuous SNP BAF values.  ...  Figure 3 . 3 Whole-Genome Single-Cell Haplotyping (A) Multi-cell and single-cell haplotypes of a disomic chromosome using discrete SNP calls before and after siCHILD analysis.  ... 
doi:10.1016/j.ajhg.2015.04.011 pmid:25983246 pmcid:PMC4473724 fatcat:fjphis5bhzazzablvo2tz4gtyi

A new distance measure for comparing sequence profiles based on path lengths along an entropy surface

G. Benson
2002 Bioinformatics  
We describe a new distance measure for comparing DNA sequence profiles.  ...  We use the new distance measure to analyze similarities within familes of tandem repeats in the C. elegans genome and show that this new measure gives more accurate refinement of family relationships than  ...  It has been a pleasure working with all three. This work was supported in part by NSF grants CCR-0073081 and DBI-0090789.  ... 
doi:10.1093/bioinformatics/18.suppl_2.s44 pmid:12385982 fatcat:dnn44zknlfdcpdoursxxmbhezi

Gene expression density profiles characterize modes of genomic regulation: Theory and experiment

Hans Binder, Henry Wirth, Jörg Galle
2010 Journal of Biotechnology  
Such 'expression spectra' were calculated and analyzed for different model genomes.  ...  Our study addresses modes of genomic regulation and their characterization using the distribution of expression values.  ...  Mutants and oncogenic de-regulation In a second series of examples we compared the gene expression profiles of wild type and mutant genomes.  ... 
doi:10.1016/j.jbiotec.2010.02.002 pmid:20156493 fatcat:yay6pck3cbednbnzjnypisrsne

An improved method for identifying functionally linked proteins using phylogenetic profiles

Shawn Cokus, Sayaka Mizutani, Matteo Pellegrini
2007 BMC Bioinformatics  
Here we propose a novel heuristic to improve phylogenetic profile analysis that accounts for phylogenetic relationships between genomes in a computationally efficient fashion.  ...  We first order the genomes within profiles and then enumerate runs of consecutive matches and accurately compute the probability of observing these.  ...  Acknowledgements We would like to acknowledge the Tavazoie laboratory for making the phylogenetic profiles and the Pagel lab for making their BayesTraits executables and bms_runner script publicly available  ... 
doi:10.1186/1471-2105-8-s4-s7 pmid:17570150 pmcid:PMC1892086 fatcat:rjylu6kbrrdcfjgv7lioje36n4

A profile likelihood analysis of the constrained MSSM with genetic algorithms

Yashar Akrami, Pat Scott, Joakim Edsjö, Jan Conrad, Lars Bergström
2010 Journal of High Energy Physics  
We present a new technique for scanning supersymmetric parameter spaces, optimised for frequentist profile likelihood analyses and based on Genetic Algorithms.  ...  Nevertheless, current data do not sufficiently constrain the model parameters in a way completely independent of priors, statistical measures and scanning techniques.  ...  [60] for useful comments on a previous version of the manuscript.  ... 
doi:10.1007/jhep04(2010)057 fatcat:gl7jieq2v5fx5fazuo7vyoyhke

Analysis of microarray experiments of gene expression profiling

Adi L. Tarca, Roberto Romero, Sorin Draghici
2006 American Journal of Obstetrics and Gynecology  
This is expected to give a mean log-ratio of zero and improve the symmetry of the data distribution.  ...  In other words, a smaller minimum detectable change will require a larger sample size.  ... 
doi:10.1016/j.ajog.2006.07.001 pmid:16890548 pmcid:PMC2435252 fatcat:aphfdrfelbdtjo42eifdzpwp3a
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