Computer applications in the biosciences : CABIOS最新文献

Motivation: Multiple molecular sequence alignment is among the most important and most challenging tasks in computational biology. The currently used alignment techniques are characterized by great computational complexity, which prevents their wider use. This research is aimed at developing a new technique for efficient multiple sequence alignment.

Approach: The new method is based on genetic algorithms. Genetic algorithms are stochastic approaches for efficient and robust searching. By converting biomolecular sequence alignment into a problem of searching for optimal or near-optimal points in an 'alignment space', a genetic algorithm can be used to find good alignments very efficiently.

Results: Experiments on real data sets have shown that the average computing time of this technique may be two or three orders lower than that of a technique based on pairwise dynamic programming, while the alignment qualities are very similar.

Availability: A C program on UNIX has been written to implement the technique. It is available on request from the authors.

Motivation: To extract the maximum possible information from a set of protein sequences, its modular organization must be known and clearly displayed. This is important both for structural and functional analysis.

Results: This paper presents an algorithm and a graphical interface called XDOM which performs a systematic analysis of the modular organization of any set of protein sequences. The algorithm is an automatic method to identify putative domains from sequence comparisons. The graphical tool displays the proteins as a set of linked boxes, corresponding to its domains. The method has been tested on a family of bacterial proteins and on whole genomes. It is currently applied to the complete SWISS-PROT database to build the PRODOM database.

Availability: XDOM is available free of charge by anonymous ftp:¿¿ftp://ftp.toulouse.inra.fr/pub/xdom¿ ¿. The ProDom database can be consulted at ¿¿http://protein.toulouse.inra.fr/prodom.html¿¿.

Motivation: DCA is a new computer program for multiple sequence alignment which utilizes a 'divide-and-conquer' type of heuristic approach.

Availability: The algorithm is freely available from http://bibiserv.TechFak.Uni-Bielefeld.DE/dca/.

Motivation: We extend the standard 'Sequence Logo' method of Schneider and Stevens (Nucleic Acids Res., 18, 6097-6100, 1990) to incorporate prior frequencies on the bases, allow for gaps in the alignments, and indicate the mutual information of base-paired regions in RNA.

Results: Given an alignment of RNA sequences with the base pairings indicated, the program will calculate the information at each position, including the mutual information of the base pairs, and display the results in a 'Structure Logo'. Alignments without base pairing can also be displayed in a 'Sequence Logo', but still allowing gaps and incorporating prior frequencies if desired.

Availability: The code is available from, and an Internet server can be used to run the program at, http://www.cbs.dtu.dk/gorodkin/appl/slogo. html.

Motivation: MacBOB (Macintosh BLAST Output Browser) and MacBOB Filter are two Macintosh-based applications that greatly simplify the viewing of BLAST and FASTA search results files.

Availability: The programs can be obtained via anonymous ftp from ftp.ri.bbsrc.ac.uk from the directory/pub/software/MacBOB, or via WWW from the Roslin Institute Home Page (http://www.ri.bbsrc.ac.uk/).

Unlabelled: A Sequence Alerting Server with a WWW interface is described which informs users with query sequences in database searches about new entries in protein databases related to their query.

Availability: The server address is http://www.bork.embl-heidelberg.de/alerting/.

This paper discusses the implementation of a three-dimensional (3D) structure motif search of proteins. Each protein structure is represented by a set of secondary structure elements (SSEs) which involves alpha-helix segments and beta-strand segments. In describing it, every SSE is further reduced into a two-node graph that consists of the starting amino acid residue, the ending residue and a pseudo-bond between them. The searching algorithm is based on a graph theoretical clique-finding algorithm that has been used for 3D substructure searching in small organic molecules. The program SS3D-P2 was validated using proteins that have well-known 3D motifs, and it correctly found the Greek key motif within an eye lens protein, crystallin, that consists of four anti-parallel beta strands. The program was also successfully applied to searching for the more complex 3D motif, TIM-type beta-barrel motif, with a protein structure database from the Protein Data Bank.