The ribonuclease P database
The Ribonuclease P Sequence database is a compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information. In its initial form, the database contains information on RNase P RNA in bacteria and archaea, and RNase P protein in bacteria. The sequences themselves are presented phylogenetically ordered and aligned. The database also contains secondary structures of bacterial and archaeal RNAs, including specially annotated 'reference' secondary structures of Escherichia coli and Bacillus subtilis RNase P RNAs, a minimum phylogenetic consensus structure, and coordinates for models of three-dimensional structure.

title: The Ribonuclease P Database
abstract: Ribonuclease P is responsible for the removal of leader sequences from tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria the RNA subunit alone is catalytically active in vitro, i.e. it is a ribozyme. The Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information, available via the World Wide Web.

title: A Macintosh Hypercard compilation of small subunit ribosomal RNA sequences
abstract: Molecular biologists, particularly those working with unicellular organisms, are becoming increasingly aware of the importance of understanding the phylogenetic (evolutionary) relationships between their model systems and other organisms. Currently, the best method for determining quantitatively the phylogenetic relationships in a group of organisms is the analysis of small subunit ribosomal RNA (ssu RNA) sequences (Woese, 1984). To assist in this type of analysis, the Ribosomal RNA Database Project (RDP) collects and distributes ssu rRNA sequences and software for phylogenetic analysis (Olsen et al., 1991). The ssu rRNA sequence stack is collection of almost 500 aligned ssu rRNA sequences taken from the first public release of the RDP sequence collection. The ssu rRNA sequence stack consists of a series of 'cards' each containing the ssu rRNA sequence of a single organism , from which the sequence can be copied (either with or without alignment information) or saved as a text file in GenBank format. Navigation in the stack is via a series of linked phylogenetic trees. Starting with a 'universal tree', clicking on the branch of interest takes the user to increasingly more specific and detailed trees. In the most specific trees, clicking on a branch either takes the user directly to the sequence card (if only one sequence is available representing that group) or presents the user with a pop-up menu of available sequences. Alternatively, the user can choose the desired sequence from a list containing the names of all of the available sequences, or choose to search the sequence names for a specific character string. The ssu rRNA sequence stack is written in Hypertalk v. 2.1, and requires v. 2.0 (or greater) of HyperCard, which in turn requires at least a Macintosh Plus, 1 Mbyte of RAM, the Macintosh operating system v 6.0.5 (or greater), and preferably a hard disk drive. The ssu rRNA sequence stack is available by anonymous FTP from ftp.bio.indiana.edu, by E-mail from the author at jwbrown@bio.indiana.edu or brownjw@iubacs.bitnet, or on floppy disk (enclose a single formatted high-density disk) free of charge on written request to the author.

title: On chromatic roots of large subdivisions of graphs
abstract: Given a graph G, we derive an expression for the chromatic polynomials of the graphs resulting from subdividing some (or all) of its edges. For special subfamilies of these, we are able to describe the limits of their chromatic roots. We also prove that for any e >0, all sufficiently large subdivisions of G have their chromatic roots in | z −1| e . A consequence of our work will be a characterization of the graphs having a subdivision whose chromatic polynomial has a root with negative real part.

title: Graph coloring satisfying restraints
abstract: For an integer k ⩾2, a proper k-restraint on a graph G is a function from the vertex set of G to the set of k -colors. A graph G is amenably k-colorable if, for each nonconstant proper k -restraint r on G , there is a k -coloring c of G with c ( v )≠ r ( v ) for each vertex v of G . A graph G is amenable if it is amenably k -colorable and k is the chromatic number of G . For any k ≠3, there are infinitely many amenable k -critical graphs. For k ⩾ 3, we use a construction of B. Toft and amenable graphs to associate a k -colorable graph to any k -colorable finite hypergraph. Some constructions for amenable graphs are given. We also consider a related property—being strongly critical —that is satisfied by many critical graphs, including complete graphs. A strongly critical graph is critical and amenable, but the converse is not always true. The Dirac join operation preserves both amenability and the strongly critical property. In addition, the Hajos construction applied to a single edge in each of two strongly k -critical graphs yields an amenable graph. However, for any k ⩾5, there are amenable k -critical graphs for which the Hajos construction on two copies is not amenable.

title: Graph properties and hypergraph colourings
abstract: Given a graph property P , graph G and integer k ⩾0, a P k -colouring of G is a function π: V ( G )→{1,..., k } such that the subgraph induced by each colour class has property P . When P is closed under induced subgraphs, we can construct a hypergraph H P G such that G is P k -colourable iff H P G is k -colourable. This correlation enables us to derive interesting new results in hypergraph chromatic theory from a ‘graphic’ approach. In particular, we build vertex critical hypergraphs that are not edge critical, construct uniquely colourable hypergraphs with few edges and find graph-to-hypergraph transformations that preserve chromatic numbers.

title: The Social Life of Documents
abstract: Documents are evolving as means for structuring and navigating information space, and resources for constructing and negotiating social space

title: The Complexity of Generalized Graph Colorings
abstract: Given a graph property P and positive integer k, a P k-coloring of a graph G is an assignment of one of k colors to each vertex of the graph so that the subgraphs induced by each color class have property P. This notion generalizes the standard definition of graph coloring, and has been investigated for many properties. We consider here the complexity of the decision problem. In particular, for the property —G, of not containing an induced subgraph isomorphic to G, we conjecture (and provide strong evidence) that —G k-colorability is NP-complete whenever G has order at least 3 and k ⩾ 2. The techniques rely on new NP-completeness results for hypergraph colorings.