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Computer Applications in the Biosciences: CABIOS

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https://www.readbyqxmd.com/read/9475994/dca-an-efficient-implementation-of-the-divide-and-conquer-approach-to-simultaneous-multiple-sequence-alignment
#1
J Stoye, V Moulton, A W Dress
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/.
December 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9475993/two-applications-to-facilitate-the-viewing-of-database-search-result-files-on-the-macintosh
#2
A S Law, D W Burt
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/).
December 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9475992/biowish-a-molecular-biology-command-extension-to-tcl-tk
#3
T Sicheritz-Pontén
No abstract text is available yet for this article.
December 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9475991/the-sequence-alerting-server-a-new-web-server
#4
H Hegyi, J M Lai, P Bork
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/.
December 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9475990/a-software-tool-for-the-analysis-of-mass-spectrometric-disulfide-mapping-experiments
#5
D Fenyö
No abstract text is available yet for this article.
December 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9475989/samba-hardware-accelerator-for-biological-sequence-comparison
#6
COMPARATIVE STUDY
P Guerdoux-Jamet, D Lavenier
MOTIVATION: SAMBA (Systolic Accelerator for Molecular Biological Applications) is a 128 processor hardware accelerator for speeding up the sequence comparison process. The short-term objective is to provide a low-cost board to boost PC or workstation performance on this class of applications. This paper places SAMBA amongst other existing systems and highlights the original features. RESULTS: Real performance obtained from the prototype is demonstrated. For example, a sequence of 300 amino acids is scanned against SWISS-PROT-34 (21 210 389 residues) in 30 s using the Smith and Waterman algorithm...
December 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9475988/xdom-a-graphical-tool-to-analyse-domain-arrangements-in-any-set-of-protein-sequences
#7
J Gouzy, P Eugéne, E A Greene, D Kahn, F Corpet
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...
December 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9475987/ss3d-p2-a-three-dimensional-substructure-search-program-for-protein-motifs-based-on-secondary-structure-elements
#8
H Kato, Y Takahashi
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...
December 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9475986/q-rt-pcr-data-analysis-software-for-measurement-of-gene-expression-by-competitive-rt-pcr
#9
P A Doris, A Hayward-Lester, J K Hays
MOTIVATION: We have developed software to assist in the computation of gene expression from data obtained in competitive reverse transcription-polymerase chain reaction (RT-PCR). This report describes the mathematical basis of competitive RT-PCR and discusses the criteria which must be met to permit accurate estimations of gene expression to be obtained using this technique. RESULTS: The software that has been developed assists in both the assessment of assay performance (specifically in establishing the equality of amplification efficiency of the native and competitor templates) and in the routine analysis of data obtained in quantitation of gene expression by competitive RT-PCR...
December 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9475985/displaying-the-information-contents-of-structural-rna-alignments-the-structure-logos
#10
J Gorodkin, L J Heyer, S Brunak, G D Stormo
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'...
December 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9475984/a-genetic-algorithm-for-multiple-molecular-sequence-alignment
#11
C Zhang, A K Wong
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...
December 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9367133/macs-automatic-counting-of-objects-based-on-shape-recognition
#12
J P Rolland, P Bon, D Thomas
No abstract text is available yet for this article.
October 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9367132/a-platform-independent-graphical-user-interface-for-seqsee-and-xalign
#13
D S Wishart, S Fortin, D R Woloschuk, W Wong, T Rosborough, G Van Domselaar, J Schaeffer, D Szafron
No abstract text is available yet for this article.
October 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9367131/pseq-gen-an-application-for-the-monte-carlo-simulation-of-protein-sequence-evolution-along-phylogenetic-trees
#14
N C Grassly, J Adachi, A Rambaut
No abstract text is available yet for this article.
October 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9367130/gsc-a-graphical-program-for-nmr-chemical-shift-comparison
#15
COMPARATIVE STUDY
W Gronwald, R F Boyko, B D Sykes
No abstract text is available yet for this article.
October 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9367129/paml-a-program-package-for-phylogenetic-analysis-by-maximum-likelihood
#16
Z Yang
No abstract text is available yet for this article.
October 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9367128/compression-of-nucleotide-databases-for-fast-searching
#17
COMPARATIVE STUDY
H Williams, J Zobel
MOTIVATION: International sequencing efforts are creating huge nucleotide databases, which are used in searching applications to locate sequences homologous to a query sequence. In such applications, it is desirable that databases are stored compactly, that sequences can be accessed independently of the order in which they were stored, and that data can be rapidly retrieved from secondary storage, since disk costs are often the bottleneck in searching. RESULTS: We present a purpose-built direct coding scheme for fast retrieval and compression of genomic nucleotide data...
October 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9367127/seqalert-a-daily-sequence-alertness-server-for-the-embl-and-swissprot-databases
#18
B Shomer
MOTIVATION: The aims were to: enable users to deposit complex search profiles against the sequence databases; interface to an independent Sequence Retrieval System (SRS) server through the network to perform these searches on a daily basis through the last day's updates of these databases; mail users the reformatted search results, enabling local usage when loaded by a WWW browser. RESULTS: The deposition of one to many search profiles by the user leads to a daily search of the EMBL and SWISSPROT databases...
October 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9367126/estimation-of-equilibrium-constants-using-automated-group-contribution-methods
#19
R G Forsythe, P D Karp, M L Mavrovouniotis
MOTIVATION: Group contribution methods are frequently used for estimating physical properties of compounds from their molecular structures. An algorithm for estimating Gibbs energies of formation through group contribution methods has been automated in an object-oriented framework. The algorithm decomposes compound structures according to a basis set of groups. It permits the use of wildcards and is able to distinguish between ring groups and chain groups that use similar search structures...
October 1997: Computer Applications in the Biosciences: CABIOS
https://www.readbyqxmd.com/read/9367125/fpc-a-system-for-building-contigs-from-restriction-fingerprinted-clones
#20
C Soderlund, I Longden, R Mott
MOTIVATION: To meet the demands of large-scale sequencing, thousands of clones must be fingerprinted and assembled into contigs. To determine the order of clones, a typical experiment is to digest the clones with one or more restriction enzymes and measure the resulting fragments. The probability of two clones overlapping is based on the similarity of their fragments. A contig contains two or more overlapping clones and a minimal tiling path of clones is selected to be sequenced. Interactive software with algorithmic support is necessary to assemble the clones into contigs quickly...
October 1997: Computer Applications in the Biosciences: CABIOS
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