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At least 127 records · Page 7Linked to original sources
PubMed1994

[Social reintegration: a dynamic program to help psychiatric patients acquire functional and interpersonal skills].

Since new mental health policies have been developed, government and community-based organizations appear to be working closer toward facilitating the social reintegration process regarding persons experiencing psychiatric problems. This article describes a project which fosters the development of a patient's functional and interpersonal skills in a para-hospital environment: supervised apartments. The program's objective is to encourage awareness of an individual's situation and especially to allow him or her to acquire and experiment a certain number of skills for the ultimate purpose of reintegrating the community. This project is carried out by the psychiatry department of Notre-Dame Hospital in collaboration with the Maison l'Echelon Inc., a non-profit organization that manages a group of supervised apartments for psychiatric patients.

Adolescent↗
PubMed1996

Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures.

We show how a basic pairwise alignment procedure can be improved to more accurately align conserved structural regions, by using variable, position-dependent gap penalties that depend on secondary structure and by taking the consensus of a number of suboptimal alignments. These improvements, which are novel for structural alignment, are direct analogs of what is possible with normal sequences alignment. They are feasible for us since our basic structural alignment procedure, unlike others, is so similar to normal sequence alignment. We further present preliminary results that show how our procedure can be generalized to produce a multiple alignment of a family of structures. Our approach is based on finding a "median" structure from doing all possible pairwise alignments and then aligning everything to it.

Amino Acid Sequence↗
PubMed2004

A memory-efficient algorithm for multiple sequence alignment with constraints.

MOTIVATION: Recently, the concept of the constrained sequence alignment was proposed to incorporate the knowledge of biologists about structures/functionalities/consensuses of their datasets into sequence alignment such that the user-specified residues/nucleotides are aligned together in the computed alignment. The currently developed programs use the so-called progressive approach to efficiently obtain a constrained alignment of several sequences. However, the kernels of these programs, the dynamic programming algorithms for computing an optimal constrained alignment between two sequences, run in (gamman2) memory, where gamma is the number of the constraints and n is the maximum of the lengths of sequences. As a result, such a high memory requirement limits the overall programs to align short sequences only. RESULTS: We adopt the divide-and-conquer approach to design a memory-efficient algorithm for computing an optimal constrained alignment between two sequences, which greatly reduces the memory requirement of the dynamic programming approaches at the expense of a small constant factor in CPU time. This new algorithm consumes only O(alphan) space, where alpha is the sum of the lengths of constraints and usually alpha << n in practical applications. Based on this algorithm, we have developed a memory-efficient tool for multiple sequence alignment with constraints. AVAILABILITY: http://genome.life.nctu.edu.tw/MUSICME.

Algorithms↗
PubMed1986

Alignment of three biological sequences with an efficient traceback procedure.

The major algorithms currently used for aligning biological sequences are those based on dynamic programming method. A dynamic programming algorithm consists of two major procedures, forward and traceback routines. This paper describes a dynamic programming algorithm for aligning three sequences at a time. Deletions and insertions are penalized according to their numbers and lengths. A forward process is accomplished in O(L3) computational steps, where L is the average sequence length. On the other hand, a traceback process is done in T steps, where T is the number of elementary configurations involved in the optimal alignment (usually T much less than L). The traceback procedure uses an effective technique for memory management, which is applicable to a wide range of sequence-matching methods.

Algorithms↗
PubMed1991

ADAPTU: animated dynamics analysis program at Tübingen University.

Molecular dynamics calculations are being used more and more in computational chemistry to investigate inter- and intra-molecular properties, as well as to determine structures. Visualization of a calculated trajectory is needed to allow a detailed analysis of the huge amount of data generated by such calculations. In addition to animating trajectories, ADAPTU was written to permit diagram generation in two and three dimensions for a detailed analysis, the extraction and listing of properties of a selected conformation and the visualization of the development of constraints in a restrained dynamics. The displayed trajectory, as well as the three-dimensional (3D) diagrams can be scaled, translated and rotated, and displayed in cross stereo representation. Our graphics device is a E&S PS300 system, which is connected to a host by Ethernet or by an asynchronous line.

Anti-Bacterial Agents↗