DIALIGN: finding local similarities by multiple sequence alignment

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DIALIGN: finding local similarities by multiple sequence alignment

MOTIVATION DIALIGN is a new method for pairwise as well as multiple alignment of nucleic 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 are not globally related,...

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Finding functional sequence elements by multiple local alignment.

Algorithms that detect and align locally similar regions of biological sequences have the potential to discover a wide variety of functional motifs. Two theoretical contributions to this classic but unsolved problem are presented here: a method to determine the width of the aligned motif automatically; and a technique for calculating the statistical significance of alignments, i.e. an assessmen...

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DIALIGN: multiple DNA and protein sequence alignment at BiBiServ

DIALIGN is a widely used software tool for multiple DNA and protein sequence alignment. The program combines local and global alignment features and can therefore be applied to sequence data that cannot be correctly aligned by more traditional approaches. DIALIGN is available online through Bielefeld Bioinformatics Server (BiBiServ). The downloadable version of the program offers several new pr...

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Multiple Sequence Alignment Using the Quasi-concave Function Optimization Based on the DIALIGN Combinatorial Structures

Multiple sequence alignment is usually considered as an optimization problem, which has a statistical and a structural component. It is known that in the problem of protein sequence alignment a processed sample is too small and not representative in the statistical sense though this information can be sufficient if an appropriate structural model is used. In order to utilize this information a ...

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DIALIGN at GOBICS—multiple sequence alignment using various sources of external information

DIALIGN is an established tool for multiple sequence alignment that is particularly useful to detect local homologies in sequences with low overall similarity. In recent years, various versions of the program have been developed, some of which are fully automated, whereas others are able to accept user-specified external information. In this article, we review some versions of the program that ...

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 1998

ISSN: 1367-4803,1460-2059

DOI: 10.1093/bioinformatics/14.3.290