AGenDA: gene prediction by cross-species sequence comparison

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AGenDA: gene prediction by cross-species sequence comparison

Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By contrast, a new class of comparative methods relies on comparing genomic sequences from evolutionary related organisms to each other. These methods are based on the concept of phylogenetic footprint...

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On Gene Prediction by Cross-Species Comparative Sequence Analysis

Sequencing of large fragments of genomic DNA makes it possible to perform comparisons of genomic sequences for identification of protein-coding regions. We have conducted a comparative analysis of homologous genomic sequences of organisms with different evolutionary distances and determined the degree of conservation of the non-coding regions between closely related organisms. In contrast, more...

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AGenDA: homology-based gene prediction

We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are...

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Prediction of gene expression specificity by promoter sequence patterns.

We present here a heuristic method toward predicting the expression specificity in the transcriptional process, which is known to be regulated in large part by promoter sequences, by observing the appearance of conserved sequence patterns in a group of known promoters, such as for housekeeping or tissue-specific genes. Statistically conserved patterns were automatically extracted from a set of ...

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Comparison of gene prediction algorithms

All three approaches share a number of common properties, which we list before going on to explore their differences: • Most algorithms locate protein-coding regions as opposed to whole genes. Nevertheless “gene prediction” remains standard nomenclature. • There is a significant amount of application-specific knowledge going into these designs. Of the systems referenced here only VEIL comes clo...

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ژورنال

عنوان ژورنال: Nucleic Acids Research

سال: 2004

ISSN: 0305-1048,1362-4962

DOI: 10.1093/nar/gkh386