Gene-Finding Approaches for Eukaryotes

Gene-finding approaches for eukaryotes.

The goal of this paper is to introduce the methods commonly used for predicting protein-coding regions in eukaryotic DNA, primarily for the benefit of those not familiar with the topic. This is not meant as a comprehensive review, nor do I describe in detail the underlying mathematical formalism. Those seeking additional information are encouraged to read some recent reviews (Fickett 1996; Clav...

AUGUSTUS: a web server for gene finding in eukaryotes

We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new method for modeling the intron length distribution. This method allows approximation of the true intron length distribution more accurately than do existing programs. For genomic sequence data from human...

CRM Finding in Higher Eukaryotes

Prediction of horizontal gene transfers in eukaryotes: approaches and challenges.

HGT (horizontal gene transfer) is recognized as an important force in bacterial evolution. Now that many eukaryotic genomes have been sequenced, it has become possible to carry out studies of HGT in eukaryotes. The present review compares the different approaches that exist for identifying HGT genes and assess them in the context of studying eukaryotic evolution. The metabolic evolution resourc...

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses

The task of gene identification frequently confronting researchers working with both novel and well studied genomes can be conveniently and reliably solved with the help of the GeneMark web software (http://opal.biology.gatech.edu/GeneMark/). The website provides interfaces to the GeneMark family of programs designed and tuned for gene prediction in prokaryotic, eukaryotic and viral genomic seq...