Syntenator: Multiple gene order alignments with a gene-specific scoring function
نویسندگان
چکیده
منابع مشابه
Finding Winner Alignments with Multiple Scoring Matrices
How to align two given sequences properly is a fundamental problem in bioinformatics. In the sequence alignment problem, the most essential thing that directly affects the resulting alignment is the scoring matrix. There are a variety of scoring matrices used for alignment, and each of them has its own purpose in biosequence alignment. It seems unlikely that an alignment is optimal for each sco...
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The multiple species de novo gene prediction problem can be stated as follows: given an alignment of genomic sequences from two or more organisms, predict the location and structure of all protein-coding genes in one or more of the sequences. Here, we present a new system, N-SCAN (a.k.a. TWINSCAN 3.0), for addressing this problem. N-SCAN can model the phylogenetic relationships between the alig...
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Sequence alignment algorithms have a long standing tradition in bioinformatics. In this paper, we formulate an extension to existing local alignment algorithms: local alignments across multiple scoring functions. For this purpose, we use the Waterman-Eggert algorithm for suboptimal local alignments as template and introduce two new features therein: 1) an alignment of two strings over a set of ...
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A necessity of repeating alignments on a same pair of sequences to select an appropriate scoring function to detect a significance of score motivates us to work on higher performance matching technique. While overlapping each alignments obtained through a set of typical scoring matrix with its default gap cost, we observe significant parameters that may induce a maximum deviation from a referen...
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UNLABELLED SNAPper is a network service for predicting gene function based on the conservation of gene order. AVAILABILITY The SNAPper server is available at http://pedant.gsf.de/snapper. SNAPper-based functional predictions will soon be offered as part of the PEDANT genome analysis server http://pedant.gsf.de.
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ژورنال
عنوان ژورنال: Algorithms for Molecular Biology
سال: 2008
ISSN: 1748-7188
DOI: 10.1186/1748-7188-3-14