levels of probes are estimated by calculating the pseudo- median or Hodge-Lehmann estimator over intensities of probes within genomic distance of bandwidth.
Jun 28, 2005 - Email: Roman R Stocsits - [email protected]; Ivo L Hofacker* - [email protected]; ... amino acid sequence when aligning coding nucleic acid sequences. ..... The Qβ replicase amplifies RNA templates autocatalyti-.
acceptor splice site candidates in multiple sequence alignments, (ii) train a support ...... We thank Thomas Derrien and Roderic Guigó for fruitful discussions.
For example, segemehl requires around 5.2 GB of virtual but only. 3.2 GB of physical ...... genome and the evolution of the chordate karyotype. Nature, 453 ...
Marc Hellmuth ...... dreier bzw. vierer Shapes ohne Pseudokanten betrachten und dabei ..... Anzahl von Knoten höher, als in dem Graphen dreier Shapes. Dieser ...
5' interaction energy, DE: upper stem energy, RE: 3' interaction energy, For each
..... Table 3, Figure 4 and Supplementary Figure S4. .... Biochimie, 84, 775–790.
Nov 11, 2008 - A shell script (runRNAsoup.sh) is available which prepares the input for. RNAsoup ... Directory containing for each internal node of .... php. 5 ...
tely 70nt precursors (pre-miRNAs) with a characteristic stem-loop structure are .... namely the miRNA families listed in the mir-base (Griffiths-. Jones, 2004 ...
Nov 11, 2008 - ... way to refine the outcome of RNAsoup. 2.1 Download - SoupViewer http://www.bioinf.uni-leipzig.de/~jane/software/soupviewer/manual. php.
the interval [â1, +1] before training, and default settings as listed. Table 1. .... Initiative (BIZ-6/1-2) of the DFG is gratefully acknowledged. REFERENCES. Chang ...
RREB-1. RXR-VDR. SAP-1. SP1. SRF. TEF. Tal1beta-E47S. USF p50 p53 p65. Figure 2: âAlignmentâ of a putative CRM of length 500 comprising 3 TFBSs (see ...
intertwined NP-hard optimization problems: the cograph editing problem, the ..... These constraints capture that Cp,q,ÎÎ = 1 as long as Mαp = Î and Mαq = Î for ...... The CPLEX Optimizer is capable of solving instances with approximately a ...
way [16]: a polymerase II transcript, the primary miRNA precursor (pri-miRNA) ... the splice sites. A related, mirtron-like source of small RNAs requires both splic- ing and ... in more than one species left 26 examples. ..... RNA family database.
Jun 10, 2014 - Institute of Computer Science. University of Leipzig. Härtelstr ... MSc, Genetics, 2nd diploma with hono
MicroRNAs and small nucleolar RNAs are thought of distinct classes of ncR- ... that snoRNAs are a prolific source of sequence fragments of microRNA size [2â.
Jun 10, 2014 - Thesis: Evolution of Conserved Non-Coding Sequences .... Hiller M, Findeià S, Nickel C, Lein S, Marz M,
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... Read Archive. Task: â¢! Convert SRA format data into FASTQ using the SRA toolkit ... -t SRR094861 -o SRR094861.qual
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Guigó et al. 1996. Page 6. Reconciliation Tree. Page 7. Evolutionary history of ...
Phylogenetics + Phylogenomics = Cophylogen_what? (part II) Maribel HernandezRosales Group of Bioinformatics University of Leipzig Vysoka '09
On the Reconstruction of the Evolutionary History of Gene Families
Phylogenetics The study of the evolution of various groups of related organisms
Gene Tree vs Species Tree
Godmann et. al. 1979
Mapping GT onto ST
Guigó et al. 1996
Reconciliation Tree
Evolutionary history of Gene Families A group of genes that are related by sequence or function similarity A set of genes originated by duplications from some ancestral gene
Identify Multiple Gene Duplications: cluster Map each node of the gene duplications and tree onto a node in the genome duplications species tree according to the LCA
Correct gene trees Infer Gene Losses and Gene and/or matrix of Duplications synteny when inconsistencies
Conclusions Synteny information: paralogy and orthology can help to improve reconstruction Allow duplication events at the leaves of the species tree More than one gene per species leads to a better clue on the gene family evolutionary history, reduces the number of introduced duplications and thus losses Allow imperfect data leads to correct the provided information
Acknowledgments Nic Wieseke Markus Riester Clara Bermudez Peter Stadler Martin Middendorf
