Historically, evolution has been studied either by looking at morphological traits in living organisms and the fossil record, or by using bioinformatics and comparative genomics. While highly useful for deducing evolutionary history, these approaches are not particularly well suited for studying the mechanisms of evolution. In order to address such issues, other methods are needed. Mathematical modelling is one of the most powerful options available, and it is the approach used in this thesis. By constructing models of biological systems, the work aims to resolve some of the many unresolved questions regarding evolutionary processes, such as how new genes evolve and how selection acts in fragmented populations. Some answers have been reached, and thus the thesis makes a small contribution to our overall understanding of evolution.. The creation of novel genes was studied both directly and by extension of an analogous system, which revolved around reversion of a frameshift mutant. The results ...
2019. Hjelmen CE, Blackmon H, Holmes VR, Burrus CG, Johnston JS. Genome Size evolution differs between Drosophila subgenera with striking differences in male and female genome size in Sophophora. accepted to g3 PDF. 2018. Hjelmen CE, Garrett M, Holmes VR, Mynes M, Piron E, and Johnston JS. Genome size evolution within and between the sexes. Journal of Heredity PDF Johnston JS, Bernardini A, Hjelmen CE. "Genome Size Estimation and Quantitative Cytogenetics in Insects." in Insect Genomics: Methods and Protocols. PDF 2017. Lower S Sander, Johnston JS, Stanger-Hall K, Hjelmen CE, Hanrahan SJ, Korunes K, and Hall D. Genome Size in North American fireflies: Substantial variation likely driven by neutral processes. GBE. PDF Hjelmen CE, and Johnston JS. The mode and tempo of genome size evolution in the subgenus Sophophora. PLOS One. PDF 2015. Arnqvist G, Sayadi A, Immonen E, Hotzy C, Rankin D, Tuda M, Hjelmen CE, and Johnston JS. Genome size correlates with reproductive fitness in seed beetles. Proc. ...
Whitney, K. D., E. J. Baack, J. L. Hamrick, M. J. W. Godt, B. C. Barringer, M. D. Bennett, C. G. Eckert, C. Goodwillie, S. Kalisz, I. J. Leitch, et al. 2010. A role for nonadaptive processes in plant genome size evolution? Evolution. 64:2097-2109 ...
To establish whether changes in genome size expansion could be indicative of polyploidy, we searched for signals of WGD in the RAD sequencing data using two-sequence-based methods: haplotype diversity per contig and bi-allelic SNP frequency distribution.. For both of these sequence-based methods, only putative coding regions were used to avoid noise. Contigs were first masked using Repeatmasker version 4.0 [31], before Blastx [32] was used to identify coding regions using default parameters and the nr (non-redundant protein sequences) database. Raw reads for all species were mapped back to these masked contigs using the BWA-mem algorithm (Burrow-Wheeler-Alignment) [33]. A contig was considered correctly assembled if both forward and reverse read of a read-pair map back to the same contig. These verified contigs were then used for all further downstream analyses.. WGD events should cause a detectable increase in haplotype diversity at individual contigs and additionally cause a shift in SNP ...
by Erin Cameron, Ph.D.. How do we learn to live well in the world? This question has intrigued me for many years now; it is why I pursued a Bachelor of Education and eventually a Ph.D. in Education. Over the last four years, my work has focused specifically on developing teaching/learning strategies that promote size diversity and acceptance. What I have learned most through this work is that how I teach is just as important as what I teach, if not sometimes more. In other words, the content alone doesnt teach, but its also how I deliver the content that significantly influences the learning experience.. Pedagogy refers to the science and art of teaching, where learning theories serve as tools for educators in order to create valuable learning experiences. When I first started teaching about size diversity I was a passionate educator wanting to change students knowledge and assumptions about weight and health. What I quickly found out is that my passion was met with strong, sometimes overt, ...
On a recent Saturday in New York City, an group of impeccably dressed women unexpectedly appeared in front of the post office on 33rd St. The city...
While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat cont…
Habitats of completely different environmental conditions harbouring azonal vegetation are connected through the contributions of water and salt. Special soil forms are usually created and maintained under permanent influence of freshwater bodies (flowing or stagnant). Similarly, increased salt concentration forms highly stressed environments, thus markedly affecting the plant composition. Those factors lead to creation of atypical vegetation in comparison to surrounding zonal vegetation. In fact, azonal vegetation in a broader sense can be divided into intrazonal i.e. vegetation that is confined to a particular type of zonal vegetation (for example Namaqualand Riviere that are unique for Succulent Karoo), or azonal sensu stricto i.e. vegetation that is common in several biomes.. ...
If I were talking in North America I would emphasize maize and wheat. But we are meeting in Asia, where rice is the major food crop. Rice is a particularly inviting target for sequencing. In the first place, it is an important crop, grown throughout the world. It feeds countless people, and it is usually eaten by people rather than fed to livestock. The world badly needs improved rice. Its great advantage for sequencing is its small genome size. It is the smallest of the cultivated grasses. Its 12 chromosomes include 430 megabases of DNA, only one sixth the number in maize, and far fewer than polyploid wheat. The green revolution brought a large increase in rice yields, but recent progress has been slower. There is room for great improvement by both standard breeding methods and by newer techniques. For example, finding QTLs in wild relatives may provide a source of new, valuable genes. It can certainly help in identifying potentially useful qualitative traits. Can we develop varieties that ...
Parasites tend to evolve small and compact genomes, generally endowed with a high mutation rate, compared with those of their free-living relatives. However, the mechanisms by which they achieve these features, independently in unrelated lineages, remain largely unknown. We argue that the loss of the classical nonhomologous end joining pathway components may be one of the crucial steps responsible for characteristic features of parasite... ...
The database is still under heavy development, several important features are not implemented yet and user interface is not finished. If having some feature request or any other comments, contact developer.. ...
TY - JOUR. T1 - Preliminary aqnalysis of length and GC content variation in the ribosomal first internal transcribed spacer (ITS1) of marine animals. AU - Chow, S.. AU - Ueno, Y.. AU - Toyokawa, M.. AU - Oohara, I.. AU - Takeyama, Haruko. PY - 2009/6. Y1 - 2009/6. N2 - Length and guanine-cytosine (GC) content of the ribosomal first internal transcribed spacer (ITS1) were compared across a wide variety of marine animal species, and its phylogenetic utility was investigated. From a total of 773 individuals representing 599 species, we only failed to amplify the ITS1 sequence from 87 individuals by polymerase chain reaction with universal ITS1 primers. No species was found to have an ITS1 region shorter than 100 bp. In general, the ITS1 sequences of vertebrates were longer (318 to 2,318 bp) and richer in GC content (56.8% to 78%) than those of invertebrates (117 to 1,613 bp and 35.8% to 71.3%, respectively). Specifically, gelatinous animals (Cnidaria and Ctenophora) were observed to have short ITS1 ...
The results of this study raise three important questions: (i) why are all bat genome sizes small relative to other mammals, (ii) why are megabat genome sizes smaller than those of microbats, and (iii) why do species of megabats differ (albeit modestly) in genome size from one another as they do?. An answer to the first question is coming into clearer focus, thanks to recent studies of all three groups of vertebrates that independently evolved powered flight. Overall, the patterns now documented in pterosaurs, birds and both major bat groups support the notion that some factor(s)-most probably including high metabolic rate-has imposed a limit on genome size in each lineage (Organ & Shedlock 2008; Andrews et al. 2009). It has recently been hypothesized that genome sizes began shrinking prior to the evolution of flight in all three groups (Organ & Shedlock 2008), which seems plausible. However, this may be difficult to test in bats (cf. dinosaurs/birds and pterosaurs; Organ et al. 2007; Organ & ...
Eukaryotic genome sizes range over five orders of magnitude. This variation cannot be explained by differences in organismic complexity (the C value paradox). To test the hypothesis that some variation in genome size can be attributed to differences in the patterns of insertion and deletion (indel) mutations among organisms, this study examines the indel spectrum inLaupala crickets, which have a genome size 11 times larger than that of Drosophila. Consistent with the hypothesis, DNA loss is more than 40 times slower in Laupala than inDrosophila. ...
Background and Aims Flow cytometry has been used to measure nuclear DNA content in pollen, mostly to understand pollen development and detect unreduced gametes. Published data have not always met the high-quality standards required for some applications, in part due to difficulties inherent in the extraction of nuclei. Here we describe a simple and relatively novel method for extracting pollen nuclei, involving the bursting of pollen through a nylon mesh, compare it with other methods and demonstrate its broad applicability and utility. Methods The method was tested across 80 species, 64 genera and 33 families, and the data were evaluated using established criteria for estimating genome size and analysing cell cycle. Filter bursting was directly compared with chopping in five species, yields were compared with published values for sonicated samples, and the method was applied by comparing genome size estimates for leaf and pollen nuclei in six species. Key Results Data quality met generally ...
The sensitivity of this procedure to resolve variation within a bacterial species is demonstrated: genome sizes and repeat structure of five environmental strains of E. coli from short Illumina reads were estimated by this method, and total genome sizes corresponded well with those obtained for the same strains by pulsed-field gel electrophoresis. In addition, this approach was applied to read-sets for completed genomes and shown to be accurate over a wide range of microbial genome sizes. ...
Reagent kit for nuclei extraction and DNA staining of nuclear DNA from animal and plant tissues to determine genome size variations and ploidy level.…
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Determining genome size and ploidy is a particularly important form of analysis in aquaculture, helping breeders select the specimens having the be...
Determining genome size and ploidy is a particularly important form of analysis in aquaculture, helping breeders select the specimens having the best…
Background: Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish. Results: Ten BAC clones of a spiny pufferfish Diodon holocanthus were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the D. holocanthus genome were identified, and 77 distinct genes were predicted. In the sequenced D. holocanthus genome, 364 kb is homologous with 265 kb of the Takifugu rubripes genome, and 223 kb is homologous with 148 kb of the Tetraodon nigroviridis genome. The repetitive DNA accounts for 8% of the sequenced D. holocanthus genome, which ...
More sets of chromosomes usually equates to more DNA. Since 1967, weve known how many chromosomes are found in the cells of most of the New Zealand hebes, but we havent known how much DNA they hold. The amount of DNA that all sets of chromosomes contain is called "genome size". Prior to this study, the genome sizes of 40 species of Veronica were known, but only one of those was from the Southern Hemisphere.. For the new study, we measured genome size in 174 individuals representing 102 species, including 54 species from New Zealand and Australia. We now know that all hebes and speedwells have relatively small genome sizes (0.26-3.19 picograms) compared to other plants and animals, roughly comparable to that of rice in this figure.. In general, Southern Hemisphere Veronica plants have more DNA (larger genomes) than most of the Northern Hemisphere species. But when we compare the amount of DNA in one chromosome set only, Southern Hemisphere Veronica plants tended to have less DNA (smaller ...
Polyploidy is a key factor in the evolution of higher plants and plays an important role in the variation of plant genomes, leading to speciation in some cases. During polyploidisation, different balancing processes take place at the genomic level that can promote variation in nuclear DNA content. We estimated genome size using flow cytometry in 84 populations of 67 Artemisia species and one population of Crossostephium chinense. A total of 73 sequences of nrDNA ITS and 3′-ETS were newly generated and analysed, together with previously published sequences, to address the evolution of genome size in a phylogenetic framework. Differences in 2C values were detected among some lineages, as well as an increase of genome size heterogeneity in subgenera whose phylogenetic relationships are still unclear. We confirmed that the increase in 2C values in Artemisia polyploids was not proportional to ploidy level, but 1Cx genome size tended to decrease significantly when high ploidy levels were reached. ...
TSC and CNI genome sizes based on the sum of chromosome sizes are close to GGA, but these sizes are smaller than those in the database [1]. The larger genome sizes were obtained from the measurement of nuclear DNA content at cellular level. Both methods differ from DNA sequencing in that they require a DNA reference point from another species. When the reference species used for nuclear measurement is distantly related from the target species, the result may be influenced by varying fluorescence intensity owing to species variation in cell or nuclear sizes. In contrast to cells, chromosome structure shows little variation between species, and human chromosomes can be used as a reference for many species, even for zebrafish [6]. Our measurement of 1.15 Gb for GGA is consistent with 1.05 Gb of the assembled sequence [19], showing that chromosome measurement has a high accuracy. Therefore, our method is to be preferred where whole-genome sequence is unavailable. Our data refine previous ...
0003] In recent years, with the support of rapid development of science and technology, a variety of cell-biological methods of estimating the genome size have been developed, such as Feulgen microscopic optical densitometry, flow cytometry and fluorescence quantitative method by using DAPI (4, 6-diamidino-2-phenylindole) staining, etc., among which flow cytometry has been used broadly. However, these methods require a relative high level of laboratory equipment and biological experimental techniques without high accuracy. For example, Feulgen microscopic optical densitometry requires a relative high level of laboratory techniques, such as preparation of control slice, selection of fixatives, control of Hydrolysis time, the role of Schiff reagent, these are all key factors to the success of the above method, which results in low accuracy. Although there are many reports of determining the genome size by flow cytometry overseas, this method is still considerable controversy. Because there are ...
Although several species have been found that are thought to have moved from being mutual partners to free-living, the reduction in genome size and host dependency means that once a relationship with the host is established, it tends to remain (occasionally breaking down into parasitism). In fact, once becoming so established that the host carried part (or all) of the bacterial genome, mutualist relationships can often evolve into organellar relationships, where the bacteria become part of the surrounding host cell, and is unable to survive on its own. Established mutualistic bacteria often lose the mobile elements that helped them establish in the first place, and the genome begins to break down as unnecessary genes are slowly lost. ...
MCB Professor Rebecca Heald is studying the effects of genome size in amphibians, where larger genomes generate larger cells, organelles, and spindle apparatus sizes during cell division. Her research seeks to identify these
IPCs Final 2015 PCB Market Size Estimates and Growth Rates Reported in North American PCB Market Report The North American PCB Market Report, published by IPC reported IPCs final estimates of 2015 market size for rigid PCBs and flexible circuits in North America. Although North American PCB production decreased 4.3 percent in 2015 to $2.9 billion, the PCB market grew 1.4 percent to an estimated $3.4 billion. READ MORE ...
Carex dudleyi, a monocot, is a perennial grasslike herb that is native to California and is endemic (limited) to California. ...
Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity
Sequencing of short-insert libraries produced 441.8 million read pairs with an average insert size of 428 bp. Analysis of the k-mer histogram at the optimal value of 55 suggested the genome size was 1.0 Gb, and the estimated Q20 read depth for this genome size was approximately 118x. Meraculous assembly using a k-mer value of 55 produced 23,275 contigs having a total length of 853.1 Mb and an N50 of 113.6 Kb. These contigs were joined by Meraculous into 14,482 scaffolds totaling 854.1 Mb in length with an N50 of 176.8 Kb and a L90 of 5,343 scaffolds. The longest Meraculous scaffold was 1.6 Mb. Meraculous estimated that the assembled contigs comprised 96% of the estimated, non-repetitive genome size and 84% of the entire genome size.. Chicago library sequencing produced 303 million read pairs, and the estimated physical coverage (the number of read pairs with inserts between 1 and 100 Kb) spanning each position in the Meraculous assembly was 382.2. HiRise made 12,824 joins and one break to the ...
Eukaryotic genomes vary remarkably in size, even between closely related species, primarily due to differences in the fraction of non-coding DNA. The existence of this variation reflects the net effects of mechanisms that expand and contract genomes, mechanisms whose balance (thus overall effects) can vary in magnitude and direction throughout evolution. Several different mechanisms have been implicated in genome size change (polyploidy, transposable element proliferation, intra-strand homologous recombination, illegitimate recombination); however, the relative importance of these mechanisms to genome size change in different lineages remains uncertain. Our research focuses on the mechanisms that influence genome size in Gossypium and the rates at which these genomes have expanded and contracted over time. Although Gossypium is a relatively young genus (~5 - 10 my) and all diploid species have the same basic chromosome number (n=13; polyploid species, n=26), the range in genome size is nearly ...
What Is An Oncidium Orchid Information About Oncidium Orchid Care. Nowadays, its quite straightforward dancing lady flower to obtain and create your own flowers using french-style in Menards. And the white flower lady may dancing lady flower add additional amazing value for your property. Apart from it appears fine...
Despite its small genome size, the Human Immunodeficiency Virus 1 (HIV-1) is one of the most successful pathogens and has infected more than 70 million people worldwide within the last decades. In total, HIV-1 expresses 16 canonical proteins from only nine genes within its 10 kb genome. Expression of the structural genes gag, pol and env, the regulatory genes rev and tat and the accessory genes vpu, nef, vpr and vif enables assembly of the viral particle, regulates viral gene transcription and equips the virus to evade or counteract host immune responses. In addition to the canonically expressed proteins, a growing number of publications describe the existence of non-canonical fusion proteins in HIV-1 infected cells. Most of them are encoded by the tat-env-rev locus. While the majority of these fusion proteins (e.g. TNV/p28tev, p186Drev, Tat1-Rev2, Tat^8c, p17tev, or Ref) are the result of alternative splicing events, Tat-T/Vpt is produced upon programmed ribosomal frameshifting, and a Rev1-Vpu fusion
What factors might have led to the L1 extinction seen here? Was it a stochastic process, or was there some change in selective forces that increased the probability of an extinction? The genomes of bats are known to be smaller than the other major groups of mammals (Bachmann 1972; Redi et al. 2005). For example, the average haploid genome size (C-value) of the 83 Chiropteran species present in the Animal Genome Size Database, Release 2.0 (Gregory 2006) is 2.55 pg, while the C-values of the 517 other mammalian species within that database average 3.57 pg. When the two suborders of the Chiroptera within that database are examined, the 7 species of Yinpterochiroptera, which include the megabats, are found to have an average C-value of 2.16 pg, while the 76 species of Yangochiroptera have an average C-value of 2.59 pg. It is known that retroelements are major contributors to increases in genome size in mammals (Kidwell 2002), so it is reasonable that reduction in L1 activity might have been a factor ...
Spanu, P. D.; Abbott, J. C.; Amselem, J.; Burgis, T. A.; Soanes, D. M.; Stüber, K.; Ver Loren van Themaat, E.; Brown, J. K. M.; Butcher, S. A.; Gurr, S. J. et al.; Lebrun, M.-H.; Ridout, C. J.; Schulze-Lefert, P.; Talbot, N. J.; Ahmadinejad, N.; Ametz, C.; Barton, G. R.; Benjdia, M.; Bidzinski, P.; Bindschedler, L. V.; Both, M.; Brewer, M. T.; Cadle-Davidson, L.; Cadle-Davidson, M. M.; Collemare, J.; Cramer, R.; Frenkel, O.; Godfrey, D.; Harriman, J.; Hoede, C.; King, B. C.; Klages, S.; Kleemann, J.; Knoll, D.; Koti, P. S.; Kreplak, J.; López-Ruiz, F. J.; Lu, X.; Maekawa, T.; Mahanil, S.; Micali, C.; Milgroom, M. G.; Montana, G.; Noir, S.; OConnell, R. J.; Oberhaensli, S.; Parlange, F.; Pedersen, C.; Quesneville, H.; Reinhardt, R.; Rott, M.; Sacristán, S.; Schmidt, S. M.; Schön, M.; Skamnioti, P.; Sommer, H.; Stephens, A.; Takahara, H.; Thordal-Christensen, H.; Vigouroux, M.; Weßling, R.; Wicker, T.; Panstruga, R.: Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in ...
J. S. Hawkins, Proulx, S. R., Rapp, R. A., and Wendel, J. F., "Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants", Proceedings of the National Academy of Sciences, vol. 106, no. 42, pp. 17811-17816, 2009. ...
The 2018 Gordon Research Conference on Genome Architecture in Cell Fate and Disease will be held in Hong Kong, China. Apply today to reserve your spot.
Available: http://www.calflora.org/ (Accessed: Dec 10, 2017). The information on this page comes from diverse sources. None of the links are sponsored. ...
Sometimes players find themselves in the position where they have to downsize. It happens to us all now and then, for whatever reason, youre heading to so...
Link: http://dx.doi.org/10.1111/ajag.12366. Butler, K., Reeve, R., Viney, R., & Burns, L. (2016). Estimating prevalence of drug and alcohol presentations to hospital emergency departments in NSW, Australia: impact of hospital consultation liaison services. Public health research & practice, 26(4), e2641642. doi: http://dx.doi.org/10.17061/phrp2641642 Retrieved from http://www.phrp.com.au/issues/september-2016-volume-26-issue-4/estimating-prevalence-of-drug-and-alcohol-presentations-to-hospital-emergency-departments-in-nsw-australia-impact-of-hospital-consultation-liaison-services/.. Butterfield, R. J., Barratt, M. J., Ezard, N., & Day, R. O. (2016). Drug checking to improve monitoring of new psychoactive substances in Australia. Medical Journal of Australia, 204(4), 144-145. doi:10.5694/mja15.01058 Retrieved from https://www.mja.com.au/journal/2016/204/4/drug-checking-improve-monitoring-new-psychoactive-substances-australia?0=ip_login_no_cache%3D52bfad2e4e141045cca76c2f2c965314.. Byrnes, J., ...
Evolutionary changes in genome size result from the combined effects of mutation, natural selection, and genetic drift. Insertion and deletion mutations (indels) directly impact genome size by adding or removing sequences. Most species lose more DNA through small indels (i.e., ∼1-30 bp) than they gain, which can result in genome reduction over time. Because this rate of DNA loss varies across species, small indel dynamics have been suggested to contribute to genome size evolution. Species with extremely large genomes provide interesting test cases for exploring the link between small indels and genome size; however, most large genomes remain relatively unexplored. Here, we examine rates of DNA loss in the tetrapods with the largest genomes-the salamanders. We used low-coverage genomic shotgun sequence data from four salamander species to examine patterns of insertion, deletion, and substitution in neutrally evolving non-long terminal repeat (LTR) retrotransposon sequences. For comparison, we ...
The base question behind the process of genome miniaturization is whether is occur trough large steps or due to a constant erosion of the gene content. In order to assess the evolution of this process is necessary to compare an ancestral genome with the one where the shrinkage is supposed to be occurred. Thanks to the similarity among the gene content of Buchnera aphidicola and the enteric bacteria Escherichia coli, 89% identity for the 16S rDNA and 62% for orthologous genes was possible to shed light on the mechanism of genome miniaturization.[33] The genome of the endosymbiont B. aphidicola is characterized by a genome size that is seven times smaller than E. coli (643 kb compared to 4.6 Mb)[34][35] and can be view as a subset of the enteric bacteria gene inventory.[35] From the confrontation of the two genomes emerged that some genes persist as partially degraded.[35] indicating that the function was lost during the process and that consequent events of erosion shortened the length as ...
Photos/images of Plants, genus Carex: Slender Tufted-Sedge - Acute Sedge (Carex acuta), Lesser Pond-Sedge (Carex acutiformis), Fibrous Tussock-Sedge (Carex appropinquata), Water Sedge (Carex aquatilis), etc.
92. Carex Caryophyllea Latourrette. Vernal Sedge Fig. 959 Carex praecox Jacq. Fl. Austr. 5: 23. pl. 446- 1778. Not Schreb. 1771. Carex caryophyllea Latourrette, Chlor. Lugdun, 27. 1785-Carex verna ...
Species: Carex turkestanica. Name. Carex turkestanica Regel. References. * Trudy Imperatorskago S.-Peterburgskago Botaniceskago Sada. Acta Horti Petropolitani. St. Petersburg 7(2):570. ...
Jen, I ran the flow as you suggested, but got following error message, Do You hav eany suggestion? I added 0 and flips the columns: Here is the few lines of input file: chr1 12137 12336 61R33AAXX100706:1:79:7707:9270 0 - chr1 31542 31741 61R33AAXX100706:1:37:11341:10600 1 - chr1 39921 40120 61R33AAXX100706:1:2:16103:17629 2 - chr1 93213 93412 61R33AAXX100706:1:113:14396:2056 3 - chr1 109395 109594 61R33AAXX100706:1:13:8451:9619 4 - chr1 146854 147053 61R33AAXX100706:1:53:15558:13513 5 - Te error message is as follow INFO @ Fri, 30 Sep 2011 17:59:54: # ARGUMENTS LIST: # name = macs_output # format = BED # ChIP-seq file = /data/CistromeAP/galaxy_database/files/000/198/dataset_198187.dat # control file = None # effective genome size = 2.79e+09 # band width = 300 # model fold = 10,30 # pvalue cutoff = 1.00e-05 # Small dataset will be scaled towards larger dataset. # Range for calculating regional lambda is: 10000 bps INFO @ Fri, 30 Sep 2011 17:59:54: #1 read tag files... INFO @ Fri, 30 Sep 2011 ...
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Steely blue coarse foliage forms a tough groundcover. Spreads agressively, but can be controlled fairly easily. Tolerates standing water.