1,721,072 research outputs found
The Number of Standard and of Effective Multiple Alignments
No full textDress A, Morgenstern B, Stoye J. The Number of Standard and of Effective Multiple Alignments. Appl. Math. Lett. 1998;11(4):43-49
DIALIGN: finding local similarities by multiple sequence alignment
No full textMorgenstern B, Frech K, Dress A, Werner T. DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics. 1998;14(3):290-294.Motivation: DIALIGN is a new method for pairwise as Well as multiple alignment oSlzucleic acid and protein sequences. While standard alignment programs rely on comparing single residues and imposing gap penalties, DIALIGN constructs alignments by comparing whole segments of the sequences. No gap penalty is employed. This point of view is especially adequate if sequences ai-e not globally related, bur share only local similarities, as is the case in genomic DNA sequences and in many protein families. Results: Using four different data sers, we show that DIALICN is able correctly to align conserved motifs in protein sequences. Alignments produced by DIALIGN are compared systematically to the results of five other alignment programs
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
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Sequenzalignment auf der Basis von Segmentvergleichen
No full textMorgenstern B. Sequenzalignment auf der Basis von Segmentvergleichen. Materialien / Universität Bielefeld, Forschungsschwerpunkt Mathematisierung, Strukturbildungsprozesse ; 105. Bielefeld; 1996
Multiple DNA and protein sequence alignment based on segment-to-segment comparison
No full textMorgenstern B, Dress A, Werner T. Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proceedings of the National Academy of Sciences of the United States. 1996;93(22):12098-12103.In this paper, a new way to think about, and to construct, pairwise as well as multiple alignments of DNA and protein sequences is proposed. Rather than forcing alignments to either align single residues or to introduce gaps by defining an alignment as a path running right from the source up to the sink in the associated dot-matrix diagram, we propose to consider alignments as consistent equivalence relations defined on the set of all positions occurring in all sequences under consideration. We also propose constructing alignments from whole segments exhibiting highly significant overall similarity rather than by aligning individual residues, Consequently, we present an alignment algorithm that (i) is based on segment-to-segment comparison instead of the commonly used residue-to-residue comparison and which (ii) avoids the well-known difficulties concerning the choice of appropriate gap penalties: gaps are not treated explicitly, but remain as those parts of the sequences that do not belong to any of the aligned segments. Finally, we discuss the application of our algorithm to two test examples and compare it with commonly used alignment methods. As a first example, we aligned a set of 11 DNA sequences coding for functional helix-loop-helix proteins. Though the sequences show only low overall similarity, our program correctly aligned all of the 11 functional sites, which was a unique result among the methods tested, As a by-product, the reading frames of the sequences were identified. Next, we aligned a set of ribonuclease EI proteins and compared our results with alignments produced by other programs as reported by McClure et al. [McClure, M. A., Vasi, T. K. & Fitch, W. M. (1994) Mol. Biol. Evol. 11, 571-592]. Our program was one of the best scoring programs. However, in contrast to other methods, our protein alignments are independent of user-defined parameters
Letters www.elsevier.com/locate/arnl A Simple and Space-Efficient Fragment-Chaining Algorithm for Alignment of DNA and Protein Sequences
No full textCommunicated by A. Dress Abstract-In the segment-based approach to sequence alignment. nucleic acid, and protein se-quence alignments are constructed from fragments, i.e., from pairs of ungapped segments of the input sequences. Given a set F of candidate fragments and a weighting function w: F + FL:, the score of an alignment is defined as the sum of weights of the fragments it consists of. and the optimiza-tion problem is to find a consistent collection of painuzse dislomt fragments wzth nmxin~um swn of wezghts. Herein, a sparse dynamic programming algorithm is described that solves the pairwise segment-alignment problem in O(L + Nmax) space where L is the maximum length of t,he input sequences while N,nax 5 #F holds. With a recently introduced weighting function 1~. small sets F of candidate fragments are sufficient to obtain alignments of high quality. As a result, the propose
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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