alignment and de novo assembly

... (see Materials and methods) in Materials and methods), and also identified small insertions or deletions (termed indels) The Velvet assembly generated from Illumina PE data alone yielded an N50 contig ... discarded 1.1 M reads containing no-call bases and 1.9 M shadow reads (described in Materials and methods) To optimize the Velvet assembly, we used alignments with our preliminary 454 and Sanger ... for sequencing and assembly We combined Sanger PE, 454 SE and Illumina PE sequence data, and developed an assembly strategy that was adaptable to evolving technologies, tools and methods Using...

Ngày tải lên: 09/08/2014, 20:20

... cooperation of Dnmt3a and Dnmt1 in de novo methylation of DNA that can only be provided by in vitro experiments In this model Dnmt3a is targeted to a domain of the DNA that is subject to de novo methylation ... Dnmt3a and Dnmt3b in maintenance methylation also has been concluded from studies with cell lines which not express functional Dnmt1 [36] and, finally, a functional interdependence of the Dnmt3a and ... methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development Cell 99, 247–257 Hsieh, C.L (2000) Dynamics of DNA methylation pattern Curr Opin Genet Dev 10, 224–228...

Ngày tải lên: 21/02/2014, 01:21

... ribbon model of human L-PGDS, which is composed of nine b-strands (strand A, Gly40–Ala49; strand B, Cys65–Ala72; strand C, Gly76–Arg85; strand D, Gln88–Pro98; strand E, Ser104–Arg108; strand F, ... strand G, Val128–Gly135; strand H, Phe143–Ser150; strand I, Ile177–Phe179) and a three-turn a-helix (Ala157–Ala169) The epitopes of MAb-5C11, MAb-10A5 and MAb-1B7 are shown in blue, orange and ... urine into the tubules and proteolytically degraded within lysosomes in the tubule cells Identification of L-PGDS of various sizes in monkey kidney and human urine We applied crude extracts of monkey...

Ngày tải lên: 30/03/2014, 01:20

... Volume 10, Issue 8, Article R88 Reference genome De novo contig De novo contig (extended) (b) De novo scaffold De novo scaffold (c) ? Probable misassembly Figure (see legend on next page) Genome ... layout, the de novo consensus module is called with standard arguments Joining scaffolds Code and assembly We used ARACHNE [14,15] to generate initial draft assemblies, and all the assisted assembly ... The assisted assembly process starts by simultaneously building a de novo assembly from the reads and by aligning the same reads to one or more related genomes These alignments provide proximity...

Ngày tải lên: 09/08/2014, 20:20

... are megakaryoblastic De novo AMKL in adulthood is rare, and carries very poor prognosis We here report a 45-year-old woman with de novo AMKL with BCR/ABL rearrangement and der(16)t(1;16)(q21;q23) ... translocation der(16)t(1;16)(q21;q23) Our case and the case reported by Kaloutsi et al [20] suggested that the FISH should be considered for detection of variant Philadelphia rearrangement in de novo ... chromosomes 22 and one yellow fusion signal on der(22)ins(22;9) To the best of our knowledge, this is the first report of de novo AMKL with rare variant of Philadelphia rearrangement and a novel...

Ngày tải lên: 10/08/2014, 21:23

... mevastatin and resveratrol treatments, and cell and nasal tissue studies JB designed all electrochemical measurement studies and interpreted those data NS provided CFTR inhibitors and aided in designing ... this study is to determine if CFTR genotype correlates with plasma membrane cholesterol detection and to determine if de novo cholesterol synthesis contributes to this measure Data demonstrate a ... study and to Nicole White and P Bead for technical assistance Author Details 1Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA, 2Department of Pediatrics and Pharmacology,...

Ngày tải lên: 12/08/2014, 11:22

... (database search, de novo peptide sequencing etc) in order to reconstruct and identify the peptide which produced it Bakhtiar and Tse [2] provides a comprehensive introduction and overview to the ... the PRM ladder or prefix ladder and similarly the set of all suffixes forms the SRM ladder or suffix ladder of the peptide The prefix and suffix ladder forms the “full ladder” of the peptide Since each ... hybrid approach into peptide identification called tag-based peptide identification which first uses de novo sequencing to get short candidate peptide fragments called peptide tags, then use these...

Ngày tải lên: 10/09/2015, 15:50

... needed by compressing various data structures such as the hash tables and sequence data 49 Conclusion De novo assembly has been a fundamental problem in biological science for the past decade and ... adapted De Bruijn graph method Therefore prior to analyzing specific algorithms, it is necessary to have a sound understanding on De Bruijn graph itself De Bruijn graph is a set of nodes and edges ... sets necessary for de novo assembly of mammalian genomes Figure 20: ABySS statistics for de novo assembly of whole human genome (Yoruba NA18507) For comparison with other de novo assemblers, the...

Ngày tải lên: 04/10/2015, 10:25

... and bad), and future Like all the books in the Taylor & Francis (formerly Marcel Dekker) Power Engineering Series, Understanding Electric Utilities and De- regulation – Second Edition puts modern ... for developing an understanding of the electric power industry and what is required to manufacture and deliver electric power to consumers Therefore, Section 1.2 begins the quest to "understand" ... power and transmission sales and service between utilities and between utilities and non-utility generators An independent agency of the Department of Energy, FERC was established in 1977, and...

Ngày tải lên: 31/12/2013, 22:00

... f1 and e2 , f2 from Phier , and concatenate them into a single phrase pair e1 e2 , f1 f2 635 Figure 1: A word alignment (a), and its derivations according to FLAT (b), and HIER (c) Solid and ... weight tuning and testing on specified development and test sets We compare the accuracy of our proposed method of joint phrase alignment and extraction using the FLAT, HIER and HLEN models, with ... For GIZA ++, we use the standard training regimen up to Model 4, and combine alignments with grow-diag-final -and For the proposed models, we train for 100 iterations, and use the final sample acquired...

Ngày tải lên: 20/02/2014, 04:20

... pages 76–82 Leonoor van der Beek, Gosse Bouma, and Gertjan van Noord 2002 Een brede computationele grammatica voor het Nederlands Nederlandse Taalkunde, 7(4):353–374 J.R Curran and M Moens 2002 Improvements ... Schuurman, and Ton van der Wouden 2000 CGN syntactische annotatie Internal Project Report Corpus Gesproken Nederlands, see http://lands let.kun.nl/cgn References R.H Baayen, R Piepenbrock, and H van ... and NRC Handelsblad 1994/1995) The corpus was parsed automatically using the Alpino parser (van der Beek et al., 2002; Malouf and van Noord, 2004) The result of parsing a sentence is a dependency...

Ngày tải lên: 20/02/2014, 12:20

... bovine submandibular gland mucins as described by Reuter and Schauer [23] Preparation of lysosomal, microsomal and cytosolic fractions from human colonic mucosa The lysosomes, microsomes and cytosol ... Neu5,7(8),9Ac3 and 4-MUAc was detected in the cytosolic and lysosomal fractions prepared from human colonic mucosa (Fig 1) OAE activities, determined using bovine submandibular gland mucin as the ... been described However, an OAE activity detected in individual bacterial strains and in faecal extracts from normal individuals, which can facilitate the action of sialidase and thus the degradation...

Ngày tải lên: 07/03/2014, 14:20

... substituted Alignment forests and alignment Alignment is the process of determining if and how a translation model generates a source, target string pair To compute an alignment under a translation model, ... addition and multiplication operation, ⊕ and ⊗, and their identities and Multiplication and addition must be associative Multiplication must distribute over addition, and v ⊗ The design of cdec separates ... BLEU and TER loss functions are provided (Papineni et al., 2002; Snover et al., 2006) Three standard algorithms parameterized with semirings are provided: I NSIDE, O UTSIDE, and I NSIDE O UTSIDE,...

Ngày tải lên: 07/03/2014, 22:20

... BotXIVM8-10, the voltage dependence was decreased both during the activation and inactivation mechanisms, in presence of BotXIV the sodium current voltage dependence was decreased only in the case ... a-like and a-insect scorpion toxins, we compared in details the primary structures of BotXIV and representative a-toxins Thus, LqqIII, BotIT1, BomIV and Bom III display 49, 53, 54, 57 and 73% identities ... potential durations under BotXIV (A) and the axonal membrane depolarization under M8-10 associated to a slight prolongation of AP duration and a AP amplitude decrease An articial repolarization...

Ngày tải lên: 08/03/2014, 23:20

... correlation between human defined comparability levels and the confidence scores derived from the comparability metric, as the Pearson R correlation scores vary between 0.966 and 0.999, depending on the ... domaindependent translation;  named entity dictionaries The demonstration showcases two general use case scenarios defined in the toolkit: “parallel data mining from comparable corpora” and “named ... comparability metrics, parallel sentence extraction and named entity/term mapping, are language independent However, they may require language dependent resources, for instance, POS-taggers, Giza++...

Ngày tải lên: 16/03/2014, 20:20

... network-based decoder Based on this decoder, we compare four commonly used word alignment methods (GIZA++, TER, CLA and IHMM) for hypothesis alignment using the same experimental data and the same ... introduces four word alignment methods, and the algorithm of computing intersection word alignment for all four word alignment methods Section describes the experiments setting and results on two ... using GIZA++ (Och and Ney, 2003) to align words between the backbone and hypothesis This method uses enhanced HMM model bootstrapped from IBM Model-1 to estimate the alignment model All hypotheses...

Ngày tải lên: 17/03/2014, 01:20

... two edges, one from bandwidth to largeur de bande., and one from bandwidth to either largeur or hap .de (type 2), or even through the two edges from bandwidth to largeur and bande (type 3), secondly, ... words, and l~ the number of English ones, where P(a,e~,f~) is the probability of observing the alignment a together with the English and French sentences, es and f~, and (a,e,f)~ -1 is a shorthand ... model on association probabilities, that we assume to be independent, the only dependencies lying in the possibilities to associate words across languages, we can simplify the above formula and...

Ngày tải lên: 17/03/2014, 07:20

... multiple RAGE-independent cell death pathways [74–76] Because of their deregulated expression, response to stress and association with neoplastic, degenerative and autoimmune disorders, S100 proteins ... these and other questions and will ultimately bring us to a higher level of understanding the biology of tumour and degeneration and enable to use our acquired knowledge of S100 structure and functions ... K, Vogl T, Fischer U, Sunderkotter C, Schulze-Osthoff K & Roth J (2007) MRP8 ⁄ MRP14 impairs endothelial integrity and induces a caspase-dependent and -independent cell death program Blood 109,...

Ngày tải lên: 23/03/2014, 03:20

... remain largely unknown Mechanisms dependent on or independent of double-strand breaks (DSBs) of DNA have both been found Here, we give an overview of the current understanding of how homologous chromosomes ... become close to each other independently of recombination (in the absence of Rec12), and these contacts are stabilized later in a recombination-dependent (Rec12-dependent) manner [16,17] Schiz ... homologous alignment obtained from recent studies in the fission yeast Schizosaccharomyces pombe and the nematode Caenorhabditis elegans, and propose models for homologous recognition Alignment...

Ngày tải lên: 29/03/2014, 08:20

... Tir and binds WASP ⁄ N-WASP to promote actin assembly Two independent studies, one that employed a genome-scale loss-of-function approach [53] and another Regulation of actin assembly by Tir and ... recent biochemical and structural studies have provided insight into the role of the tandem repeat configuration in EspFU signaling BAR hopping: membrane-deforming proteins and pedestal formation ... three tandem SH3 domains of Nck1 and Nck2 likely activate N-WASP by directly binding to its PRD Multimerization of N-WASP can further enhance Arp2 ⁄ 3-mediated actin nucleation and pedestal assembly...

Ngày tải lên: 29/03/2014, 09:20