NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of genomic, transcript and protein sequence records. These records are selected and curated from public sequence archives and represent a significant reduction in redundancy compared to the volume of data archived by the International Nucleotide Sequence Database Collaboration. The database includes over 16 000 organisms, 2.4 × 106 genomic records, 13 × 106 proteins and 2 × 106 RNA records spanning prokaryotes, eukaryotes and viruses (RefSeq release 49, September 2011). The RefSeq database is maintained by a combined approach of automated analyses, collaboration and manual curation to generate an up-to-date representation of the sequence, its features, names and cross-links to related sources of information. We report here on recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline. More information about the resource is available online (see http://www.ncbi.nlm.nih.gov/RefSeq/)

Bilateral negotiation in a multi-agent supply chain system

A supply chain is a set of organizations directly linked by flows of services from suppliers to customers. Supply chain activities range from the ordering and receipt of raw materials to the production and distribution of finished goods. Supply chain management is the integration of key activities across a supply chain for the purposes of building competitive infrastructures, synchronizing supply with demand, and leveraging worldwide logistics. This paper addresses the challenges created by supply chain management towards improving long-term performance of companies. It presents a multi-agent supply chain system composed of multiple software agents, each responsible for one or more supply chain activities, and each interacting with other agents in the execution of their responsibilities. Additionally, this paper presents the key features of a negotiation model for software agents. The model handles bilateral multi-issue negotiation and incorporates an alternating offers protocol, a set of logrolling strategies, and a set of negotiation tactics

An analysis of integrative outcomes in the Dayton peace negotiations

The nature of the negotiated outcomes of the eight issues of the Dayton Peace Agreement was studied in terms of their integrative and distributive aspects. in cases where integrative elements were Sound, further analysis was conducted by concentrating on Pruitt's five types of integrative solutions: expanding the pie, cost cutting, non-specific compensation, logrolling, and bridging. The results showed that real world international negotiations can arrive at integrative agreements even when they involve redistribution of resources tin this case the redistribution of former Yugoslavia). Another conclusion was that an agreement can consist of several distributive outcomes and several integrative outcomes produced by different kinds of mechanisms. Similarly, in single issues more than one mechanism can be used simultaneously. Some distributive bargaining was needed in order to determine how much compensation was required. Finally, each integrative formula had some distributive aspects as well

DNA replication stress restricts ribosomal DNA copy number

Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100–200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how “normal” copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a “normal” rDNA copy number

NCBI Reference Sequences: current status, policy and new initiatives

NCBI's Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. RefSeq records integrate information from multiple sources and represent a current description of the sequence, the gene and sequence features. The database includes over 5300 organisms spanning prokaryotes, eukaryotes and viruses, with records for more than 5.5 × 106 proteins (RefSeq release 30). Feature annotation is applied by a combination of curation, collaboration, propagation from other sources and computation. We report here on the recent growth of the database, recent changes to feature annotations and record types for eukaryotic (primarily vertebrate) species and policies regarding species inclusion and genome annotation. In addition, we introduce RefSeqGene, a new initiative to support reporting variation data on a stable genomic coordinate system

Human immunodeficiency virus type 1, human protein interaction database at NCBI

The ‘Human Immunodeficiency Virus Type 1 (HIV-1), Human Protein Interaction Database’, available through the National Library of Medicine at www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions, was created to catalog all interactions between HIV-1 and human proteins published in the peer-reviewed literature. The database serves the scientific community exploring the discovery of novel HIV vaccine candidates and therapeutic targets. To facilitate this discovery approach, the following information for each HIV-1 human protein interaction is provided and can be retrieved without restriction by web-based downloads and ftp protocols: Reference Sequence (RefSeq) protein accession numbers, Entrez Gene identification numbers, brief descriptions of the interactions, searchable keywords for interactions and PubMed identification numbers (PMIDs) of journal articles describing the interactions. Currently, 2589 unique HIV-1 to human protein interactions and 5135 brief descriptions of the interactions, with a total of 14 312 PMID references to the original articles reporting the interactions, are stored in this growing database. In addition, all protein–protein interactions documented in the database are integrated into Entrez Gene records and listed in the ‘HIV-1 protein interactions’ section of Entrez Gene reports. The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication

Hausdorff dimension of operator semistable L\'evy processes

Let $X=\{X(t)\}_{t\geq0}$ be an operator semistable L\'evy process in \rd with exponent $E$, where $E$ is an invertible linear operator on \rd and $X$ is semi-selfsimilar with respect to $E$. By refining arguments given in Meerschaert and Xiao \cite{MX} for the special case of an operator stable (selfsimilar) L\'evy process, for an arbitrary Borel set B\subseteq\rr_+ we determine the Hausdorff dimension of the partial range $X(B)$ in terms of the real parts of the eigenvalues of $E$ and the Hausdorff dimension of $B$.Comment: 23 page

Fractal-dimensional properties of subordinators

This work looks at the box-counting dimension of sets related to subordinators (non-decreasing Lévy processes). It was recently shown in Savov (Electron Commun Probab 19:1–10, 2014) that almost surely limδ→0U(δ)N(t,δ)=t , where N(t,δ) is the minimal number of boxes of size at most δ needed to cover a subordinator’s range up to time t, and U(δ) is the subordinator’s renewal function. Our main result is a central limit theorem (CLT) for N(t,δ) , complementing and refining work in Savov (2014). Box-counting dimension is defined in terms of N(t,δ) , but for subordinators we prove that it can also be defined using a new process obtained by shortening the original subordinator’s jumps of size greater than δ . This new process can be manipulated with remarkable ease in comparison with N(t,δ) , and allows better understanding of the box-counting dimension of a subordinator’s range in terms of its Lévy measure, improving upon Savov (2014, Corollary 1). Further, we shall prove corresponding CLT and almost sure convergence results for the new process