6,089 research outputs found
New journal: Algorithms for Molecular Biology
No full textAbstract This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we provide a forum for fast publication of high-quality research articles in this rapidly evolving field. Our journal will publish thoroughly peer-reviewed papers without length limitations covering all aspects of algorithmic data analysis in computatioal biology. Publications in Algorithms for Molecular Biology are easy to find, highly visible and tracked by organisations such as PubMed. An established online submission system makes a fast reviewing procedure possible and enables us to publish accepted papers without delay. All articles published in our journal are permanently archived by PubMed Central and other scientific archives. We are looking forward to receiving your contributions.</p
Generic Properties Of The Sequence-Structure Relations Of Biopolymers
No full textntaining all ff n possible genotypes of given chain length n, where ff denotes the size of the polynucleotide or amino acid alphabet. Distances in sequence space are expressed by the minimum number of single nucleotide exchanges or point mutations 2 PETER F. STADLER SEQUENCE SPACE SHAPE SPACE PARAMETER SPACE (Fitness Values) CONCENTRATIION SPACE Population Dynamics Support Dynamics the environment evaluation by folding, morphogenesis Figure 1. Evolutionary dynamics. In vitro evolution of biomolecules is partitioned into four components: (i) population dynamics, (ii) population support dynamics, (iii) genotype -phenotype mapping, and (iv) evaluation of the phenotype. Wright's notion of a fitness landscape is the composite of genotype-phenotype mapping and phenotype evaluation (shaded in gray). Population dynamics is tantamount to chemical reactio
Joseph Bimeler book order to Peter Kaufmann, February 14, 1845
No full textOrder of two dozen German A.B.C. books (primers) by J.M. Bimeler (by Lewis F. Birk) from Peter Kaufmann.
Led by Joseph Bimeler (sometimes spelled Bäumeler) in 1817, a group of Lutheran separatists left Germany and eventually established the small community of Zoar in Tuscarawas County, Ohio. The group formed the Society of Separatists of Zoar, in which each person donated his or her property to the community as a whole, and in exchange for their work, the society would provide for them. After decades of economic prosperity, the unity of the village declined, and by 1898 the Zoarites disbanded the society.
Peter Kaufmann was a German immigrant and intellectual. He arrived first in Philadelphia, Pennsylvania, in 1820; in 1826 he became professor of languages at the Harmony Society town of Economy, Pennsylvania. In 1827, Kaufmann led the establishment of Teutonia, a utopian community in Columbiana County, Ohio, and published its weekly titled "Teutonia: The Herald of a Better Time." Following this he moved to Canton, Ohio, where he became translator and editor of "Der Vaterlandsfreund und Geist der Zeit" under Solomon Sala. Additionally, Kaufmann wrote a number of books on education, as well as a German almanac. He was also an influential Democrat, counting President Van Buren among his friends, and knew Ralph Waldo Emerson
Comparative RNA Genomics
No full textOver the last quarter of a century it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large-scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible non-coding RNAs that exert a vastly diverse array of molecule functions. In this chapter we provide a-necessarily incomplete-overview of the current state of comparative analysis of non-coding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world.</p
Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster
No full textA computational screen for novel small nucleolar RNAs in Drosophila melanogaster uncovered 15 novel snoRNAs and snoRNA-like long non-coding RNAs. In contrast to earlier surverys, the novel sequences are mostly poorly conserved and originate from unusual genomic locations. The majority derive from precurors antisense to well-known protein-coding genes, and four of the candidates are produced from exon-coding regions. Only a minority of the new sequences appears to have canonical target sites in ribosomal or small nuclear RNAs. Taken together, these evolutionary young, poorly conserved, and genomically atypical sequences point at a class of snoRNA-like transcripts with predominantly regulatory functions in the fruit fly genome
Multiple sequence alignment with user-defined anchor points
No full textBackground: Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments. Results: Herein, we describe a semi-automatic version of the alignment program DIALIGN that can take pre-defined constraints into account. It is possible for the user to specify parts of the sequences that are assumed to be homologous and should therefore be aligned to each other. Our software program can use these sites as anchor points by creating a multiple alignment respecting these constraints. This way, our alignment method can produce alignments that are biologically more meaningful than alignments produced by fully automated procedures. As a demonstration of how our method works, we apply our approach to genomic sequences around the Hox gene cluster and to a set of DNA-binding proteins. As a by-product, we obtain insights about the performance of the greedy algorithm that our program uses for multiple alignment and about the underlying objective function. This information will be useful for the further development of DIALIGN. The described alignment approach has been integrated into the TRACKER software system
Maximum likelihood estimation of weight matrices for targeted homology search
No full textGenome annotation relies to a large extent on the recognition of homologs to already known genes. The starting point for such protocols is a collection of known sequences from one or more species, from which a model is constructed – either automatically or manually – that encodes the defining features of a single gene or a gene family. The quality of these models eventually determines the success rate of the homology search. We propose here a novel approach to model construction that not only captures the characteristic motifs of a gene, but are also adjusts the search pattern by including phylogenetic information. Computational tests demonstrate that this can lead to a substantial improvement of homology search models
Composting of aged reed bed biosolids for beneficial reuse: a case study in New Jersey, USA
No full textReed beds with Phragmites australis (common reed) have been utilized to decrease the water, nutrient and volatile solids content of sewage sludge. An efficient disposal/reuse option was sought for reed bed biosolids accumulated over a 15 year period at a wastewater treatment facility in New Jersey, USA. The study facility had 14 reed beds, each with 1000 wet tons capacity, which were full, and so the solids needed to be removed. Because P. australis is considered an invasive species in New Jersey and several other states in the United States, disposal or reuse of solids containing this plant is regulated. Composting was examined as a potential treatment for destroying the plant’s reproductive rhizomes. The high temperatures achieved during composting were also tested to determine if regulatory criteria for pathogen reduction could be met, making the composted product suitable for unrestricted land application. Preliminary studies indicated the sludge had stabilized to the point where self-heating did not occur. Among the carbon amendments tested in the laboratory to stimulate compositing activity, Phragmites above ground biomass was determined to be most suitable. In a field test, Phragmites above ground biomass was mixed with reed bed biosolids at a 1:2 (w/w) ratio. The temperatures achieved resulted in complete mortality of Phragmites rhizomes. In laboratory tests, rhizomes placed in a drying oven at 50ºC for 24 hours, or 55ºC for 12 hours, showed 100% plant mortality. However, under field conditions pile temperatures could not be maintained long enough for the sludge to meet the USEPA 503 biosolids time-temperature pathogen rule requirements for unrestricted land application, even though sample fecal coliform counts did meet regulatory limits.Peer reviewed
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