Methodology for Constructing Problem Definitions in Bioinformatics

Motivation: A recurrent criticism is that certain bioinformatics tools do not account for crucial biology and therefore fail answering the targeted biological question. We posit that the single most important reason for such shortcomings is an inaccurate formulation of the computational problem. Results: Our paper describes how to define a bioinformatics problem so that it captures both the underlying biology and the computational constraints for a particular problem. The proposed model delineates comprehensively the biological problem and conducts an item-by-item bioinformatics transformation resulting in a germane computational problem. This methodology not only facilitates interdisciplinary information flow but also accommodates emerging knowledge and technologies

The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region

To gain insight into the mitochondrial genome structure and gene content of a putatively ancestral group of eukaryotes, the cryptophytes, we sequenced the complete mitochondrial DNA of Rhodomonas salina. The 48 063 bp circular-mapping molecule codes for 2 rRNAs, 27 tRNAs and 40 proteins including 23 components of oxidative phosphorylation, 15 ribosomal proteins and two subunits of tat translocase. One potential protein (ORF161) is without assigned function. Only two introns occur in the genome; both are present within cox1 belong to group II and contain RT open reading frames. Primitive genome features include bacteria-like rRNAs and tRNAs, ribosomal protein genes organized in large clusters resembling bacterial operons and the presence of the otherwise rare genes such as rps1 and tatA. The highly compact gene organization contrasts with the presence of a 4.7 kb long, repeat-containing intergenic region. Repeat motifs ∼40–700 bp long occur up to 31 times, forming a complex repeat structure. Tandem repeats are the major arrangement but the region also includes a large, ∼3 kb, inverted repeat and several potentially stable ∼40–80 bp long hairpin structures. We provide evidence that the large repeat region is involved in replication and transcription initiation, predict a promoter motif that occurs in three locations and discuss two likely scenarios of how this highly structured repeat region might have evolved

and complex repeat region

bacteria-like operons, compact gene arrangemen

Jet and underlying event properties as a function of charged-particle multiplicity in proton–proton collisions at √s = 7 TeV

Abstract Characteristics of multi-particle production in proton-proton collisions at √s = 7 TeV are studied as a function of the charged-particle multiplicity, N ch. The produced particles are separated into two classes: those belonging to jets and those belonging to the underlying event. Charged particles are measured with pseudorapidity |η|0.25 GeV/c. Jets are reconstructed from charged-particles only and required to have pT>5 GeV/c. The distributions of jet pT, average pT of charged particles belonging to the underlying event or to jets, jet rates, and jet shapes are presented as functions of Nch and compared to the predictions of the pythia and herwig event generators. Predictions without multi-parton interactions fail completely to describe the Nch-dependence observed in the data. For increasing Nch, pythia systematically predicts higher jet rates and harder pT spectra than seen in the data, whereas herwig shows the opposite trends. At the highest multiplicity, the data–model agreement is worse for most observables, indicating the need for further tuning and/or new model ingredients