Computer applications in the biosciences : CABIOS最新文献

Motivation: The increasing availability of biological databases on the World-Wide Web and hypertext links between them has made a wealth of information easily accessible to biologists. Additional retrieval capabilities can be achieved by storing explicitly specified biological relationships between different entities as discrete database entries.

Results: We have built CySPID, a prototype database about the cytoskeleton that explores the approach of explicitly representing biological relationships. The stored relationships are displayed along with other retrieved information, can be used to make hyperlinks to related entities, and can be used to search for entities with specified properties. CySPID is extensible in that new types of relationships may be created without altering the database schema.

Availability: CySPID is available for public use (http://ycmi.med.yale.edu/cyspid/). The CGI scripts used by CySPID are available upon request.

Motivation: Most protein sequence alignment algorithms give similar results on closely related proteins, while manual intervention may be needed for distantly related molecules. To correct the alignment, it is often necessary to repeat calculations on selected parts of the alignments and edit the alignment manually. Software implementing such interactive alignment procedures is of significance.

Results: This paper presents a new MS Windows application called ProMSED for both automatic and manual protein sequence alignment. The program reads main sequence formats and has a user-friendly interface. ProMSED performs automatic (ClustalV algorithm) alignments, alignment visualization and editing, and it allows sequences to be aligned interactively leaving previously aligned regions unchanged. Manual alignment and sequence analysis are facilitated by colouring schemes reflecting amino acid similarity of mutational and physicochemical properties. The interactive alignment of a diverged set of reverse transcriptases has located four out of six known conserved motifs.

Availability: ProMSED is available on request from the authors. DEMO is available from ftp://ftp.ebi.ac.uk/pub/ software/dos/promsed/ or ftp://iubio.bio.indiana.edu/molbio/ ibmpc/.

Motivation: The secondary structure is a key element of architectural organization in proteins. Accurate assignment of the secondary structure elements (SSE) (helix, strand, coil) is an essential step for the analysis and modelling of protein structure. Various methods have been proposed to assign secondary structure. Comparative studies of their results have shown some of their drawbacks, pointing out the difficulties in the task of SSE assignment.

Results: We have designed a new automatic method, named P-SEA, to assign efficiently secondary structure from the sole C alpha position. Some advantages of the new algorithm are discussed.

Availability: The program P-SEA is available by anonymous ftp: ftp.lmcp.jussieu.fr directory: pub/.

Motivation: Phylogenetic trees constructed from molecular sequences contain information about the evolutionary or population dynamical processes that created them. Here we describe a computer package (End-Epi) that uses graphical methods to allow researchers to make inferences about these processes from their data. Statistical analyses can be performed to test the consistency of the data with various competing hypotheses.

Availability: End-Epi can be obtained by WWW from http://evolve.zoo.ox.ac.uk/ and by anonymous FTP from ftp://evolve.zoo.ox.ac.uk/packages/End-Epi10.hqx. This file contains the compiled application, the manual and a test tree.

Motivation: When inspecting two maps of a chromosome or chromosomal region derived by similar or different methodologies, a computer-generated description of their differences is valuable, both to guide laboratory research as well as to assist version control. Our program, Mapdiff, can be used to compare two independently derived maps, or two revisions of the same map. Its usefulness increases in proportion to the percentage of shared objects between the two maps. Mapdiff uses a greedy algorithm to determine differences between shared objects.

Results: We illustrate Mapdiff's use in comparing the publicly available STS-content and radiation hybrid maps of human chromosome 12.

Availability: Freely available, (source, executables for Windows/DOS and Sun Solaris, documentation) on request from the author.

Motivation: Compression algorithms can be used to analyse genetic sequences. A compression algorithm tests a given property on the sequence and uses it to encode the sequence: if the property is true, it reveals some structure of the sequence which can be described briefly, this yields a description of the sequence which is shorter than the sequence of nucleotides given in extenso. The more a sequence is compressed by the algorithm, the more significant is the property for that sequence.

Results: We present a compression algorithm that tests the presence of a particular type of dosDNA (defined ordered sequence-DNA): approximate tandem repeats of small motifs (i.e. of lengths < 4). This algorithm has been experimented with on four yeast chromosomes. The presence of approximate tandem repeats seems to be a uniform structural property of yeast chromosomes.

Motivation: This paper summarizes a biological key using a fuzzy logic expert system. This approach allows the user to make some errors, be uncertain about some answers and not answer questions if unsure, but have an opportunity to identify unknown specimens correctly. This approach was adopted in order to develop a 'forgiving' key for users with little or no prior knowledge of identification. The system was implemented using a multi-media expert system builder, 'Matcher', operating in a Microsoft Windows environment.

Results: The paper reports the design issues for a key to identify freshwater invertebrates to family level and describes the types of questions used within the key, the fuzzy inference engine, the structure of the system and the methodology adopted for testing it. Following this, an empirical test is reported of the hypothesis that a fuzzy logic expert system can improve identification accuracy for a sample of intended users. Finally, the discussion considers the practicalities of using such a system as an aid to organism identification.