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Waiting times for clumps of patterns and for structured motifs in random sequences

V.T. Stefanov, S. Robin, S. Schbath
2007 Discrete Applied Mathematics  
This paper provides exact probability results for waiting times associated with occurrences of two types of motifs in a random sequence.  ...  Second, we provide explicit expressions for the probability generating functions of both the waiting time until the first occurrence, and the interarrival time between consecutive occurrences, of a structured  ...  As we did in Section 2.3 for the number of clumps, the above theorem can be used to get the p.g.f. of the number of occurrences of a structured motif in a random sequence.  ... 
doi:10.1016/j.dam.2005.07.016 fatcat:dfvte2iwwng4fdjns5377a6hge

Probabilistic Arithmetic Automata and their Applications [article]

Tobias Marschall and Inke Herms and Hans-Michael Kaltenbach and Sven Rahmann
2010 arXiv   pre-print
Here, we present five different applications, namely (1) pattern matching statistics on random texts, including the computation of the distribution of occurrence counts, waiting time and clump size under  ...  DAAs) to model deterministic calculations on sequences, and demonstrate how to construct a PAA from a given DAA and a finite-memory random text model.  ...  IH was supported by the NRW Graduate School in Bioinformatics and Genome Research, Bielefeld.  ... 
arXiv:1011.5778v1 fatcat:revdhc7rt5gvvhxlfj6bxnsanm

Martingale Methods for Patterns and Scan Statistics [chapter]

Vladimir Pozdnyakov, J. Michael Steele
2009 Scan Statistics  
We show how martingale techniques (both old and new) can be used to obtain otherwise hard-to-get information for the moments and distributions of waiting times for patterns in independent or Markov sequences  ...  In particular, we show how these methods provide moments and distribution approximations for certain scan statistics, including about variable length scan statistics.  ...  Introduction The martingale method for waiting times for patterns in an independent sequence was pioneered in Li (1980) , and in the intervening time many variations on the original idea have been developed  ... 
doi:10.1007/978-0-8176-4749-0_14 fatcat:loqgiidpqreulljmjyr6xybh3y

Mendelian microsatellite loci for the Caribbean coral Acropora palmata

IB Baums, CR Hughes, ME Hellberg
2005 Marine Ecology Progress Series  
Genetic estimates of population connectivity and clonal structure should be part of these efforts, but such studies have been hampered by low levels of mitochondrial DNA variation in corals, and an apparent  ...  We developed 8 polymorphic microsatellite markers for A. palmata, and performed crosses to confirm co-dominant inheritance patterns.  ...  Random numbers were generated for each of 3 nested circles with radii of 15, 10 and 5 m. The random numbers generated were precise to 5°of arc and 50 cm along strike.  ... 
doi:10.3354/meps288115 fatcat:bullrtf6jze6djwkwttgmwrfpi

The Origins of Eukaryotic Gene Structure

Michael Lynch
2005 Molecular biology and evolution  
To address these issues, a general hypothesis for the emergence of eukaryotic gene structure is provided here.  ...  drive patterns of gene expression, and expansive intergenic regions that harbor additional diffuse control mechanisms.  ...  Koonin and F. Kondrashov for important comments that led to significant improvement of this presentation. J. Conery helped in procuring the prokaryotic genome content data.  ... 
doi:10.1093/molbev/msj050 pmid:16280547 fatcat:dzburtucqbeabjcvq5rowmnyoy

Neoproterozoic microbialites in outcrops of the Qarn Alam salt dome, central Oman

Monique Mettraux, Peter Homewood, Said Al Balushi, Marcelle Marques Erthal, Nilo Siguehiko Matsuda
2014 GeoArabia  
Both calcitic and dolomitic phases show microbial fossils and structures with fabrics of mineralised extra-cellular polymeric substances (EPS).  ...  Whereas dolomite shows no post-depositional diagenetic modification and records preservation of finely detailed EPS mineralisation, the calcite of clumps of clots and mesoclots shows neomorphism with reorganisation  ...  Employees at PDO's Geomatics Section are appreciated for their assistance in digitizing and drafting the geological map of the Qarn Alam Salt Dome.  ... 
doi:10.2113/geoarabia190317 fatcat:hcjqbzkv75dfvf2nyhiia6sl3a

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

E. E. Schadt, O. Banerjee, G. Fang, Z. Feng, W. H. Wong, X. Zhang, A. Kislyuk, T. A. Clark, K. Luong, A. Keren-Paz, A. Chess, V. Kumar (+4 others)
2012 Genome Research  
By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information  ...  DNA sequencing carried out using current first and second (or next) generation sequencing (NGS) instruments has achieved significant success in providing DNA sequences in which the A's, G's, C's, and T's  ...  Acknowledgments This study was partially supported by the US National Institutes of Health grant 1RC2HG005618-01.  ... 
doi:10.1101/gr.136739.111 pmid:23093720 pmcid:PMC3530673 fatcat:pn5ywzxb5jgxrfmw5h5ehzhaie

45th European Mathematical Genetics Meeting (EMGM) 2017, Tartu, Estonia, April 4-7, 2017: Abstracts

2016 Human Heredity  
In addition to GWAS results, these approaches require estimates of genotype-genotype and/or phenotype-phenotype covariance structures to properly account for dependences between variables.  ...  I consider these questions in the context of our recent multivariate methods metaCCA and FINEMAP.  ...  The probability of calling position as a de novo mutation in a trio we calculate independently for each family. Assuming independence, we calculate probability of  ... 
doi:10.1159/000469638 pmid:28376496 fatcat:e4rysb6hsreetptmgexr3xvjou

Poster Presentations April 1–5, 2009

2009 Cellular Oncology  
These 3'UTR derived transcripts, which we term utRNAs, contain specific sequence motifs and structure.  ...  patients whom will benefit of a 'wait-and-scan' approach.  ...  Conclusions: Apparently random patterns of mutation and gene expression change in cancers closely follow the underlying chromatin landscape.  ... 
doi:10.1155/2009/694596 doaj:93d0747999384264903dbf7ede23bc34 fatcat:znrwarewrfhx7nmp3wyn62r5eq

Genomes 2000 International Conference on Microbial and Model Genomes

Jo Wixon
2000 Yeast  
There are genomes of all shapes and sizes out there waiting to be sequenced and many genes whose functions we have yet to determine.  ...  projects reported back on progress and described future plans, researchers using structural genomics demonstrated the power of this technique both in the lab and at the computer, and those working on  ...  There are genomes of all shapes and sizes out there waiting to be sequenced and many genes whose functions we have yet to determine.  ... 
doi:10.1002/1097-0061(20000630)17:2<124::aid-yea23>3.0.co;2-l fatcat:bhlv3zq67vf5tpoa37e4jodjvq

Spatial genetic analysis reveals high connectivity of tiger (Panthera tigris) populations in the Satpura-Maikal landscape of Central India

Sandeep Sharma, Trishna Dutta, Jesús E. Maldonado, Thomas C. Wood, Hemendra Singh Panwar, John Seidensticker
2013 Ecology and Evolution  
We investigated the spatial genetic structure of the tiger meta-population in the Satpura-Maikal landscape of central India using population-and individualbased genetic clustering methods on multilocus  ...  However, deforestation, road widening, and mining may sever this connectivity, impede gene exchange, and further exacerbate the genetic division of tigers in central India.  ...  Shouche and Hitendra Munot of the National Center for Cell Sciences, Pune, India, for providing laboratory space and facilitating the lab work.  ... 
doi:10.1002/ece3.432 pmid:23403813 pmcid:PMC3568842 fatcat:ph6xkwxnvzguhg7whq6z37eslm

RNA LOCALIZATION IN DEVELOPMENT

Arash Bashirullah, Ramona L. Cooperstock, Howard D. Lipshitz
1998 Annual Review of Biochemistry  
Cytoplasmic RNA localization is an evolutionarily ancient mechanism for producing cellular asymmetries. This review considers RNA localization in the context of animal development.  ...  In Drosophila, localized RNAs program the anteroposterior and dorso-ventral axes of the oocyte and embryo.  ...  [U(G/A)U(A/G)U(G/A)U] important for Bruno binding The importance of RNA secondary structure in localization has been clear for some time (e.g. bicoid 3 -UTR) (166, 167) .  ... 
doi:10.1146/annurev.biochem.67.1.335 pmid:9759492 fatcat:bhmb6tc4yfc2zhqrnyvp72bj2i

Effects of the social environment during adolescence on the development of social behaviour, hormones and morphology in male zebra finches (Taeniopygia guttata)

Stefanie Bölting, Nikolaus von Engelhardt
2017 Frontiers in Zoology  
In many vertebrates the effects of social interactions early in life on adult behaviour are mediated by changes in maturation and physiology.  ...  Individual differences in behaviour are widespread in the animal kingdom and often influenced by the size or composition of the social group during early development.  ...  Ursula Rennemann for taking care of the animals, Sabine Kruse, Tanja Möllers and Sylvia Kaiser for hormone analyses, Anja Günther for statistical advice, Anja Günther, Tobias Krause and Sylvia Kaiser  ... 
doi:10.1186/s12983-017-0190-4 pmid:28149319 pmcid:PMC5267386 fatcat:wkccdhu3ijegxlksrip7qf2xz4

An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges

P. Chain
2003 Briefings in Bioinformatics  
Understanding gene function, gene regulation, gene networks, phylogenetic studies and other aspects of evolution all depend on accurate nucleic acid and protein sequence alignment.  ...  Selecting appropriate tools can make a large difference in the quality of results obtained and the effort required.  ...  Thanks also to Burkhard Morgenstern for his suggestions improving the description of DIALIGN.  ... 
doi:10.1093/bib/4.2.105 pmid:12846393 fatcat:3p5ybliqe5earn3hz4bmatuljy

'New Arts, New Worlds!': Strindberg and Painting [chapter]

Michael Robinson
2013 Studies in Strindberg  
at is what Buddha is waiting for! [SV 58, 212] No doubt! And most eloquent!  ...  had to wait until 1906 for its rst professional production in Sweden), he returned to painting and also sculpted, while staying among artist friends at the resort of Dalarö, south of Stockholm.  ... 
doi:10.5334/bac.j fatcat:vhvghycimbcerhpcq53nfebwly
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