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  • Web report
  • Open Access

Gene identification software

Genome Biology20001:reports2053

https://doi.org/10.1186/gb-2000-1-3-reports2053

  • Received: 2 August 2000
  • Published:

Abstract

The GRAIL server is one of the many internet resources for predicting genes in uncharacterized genomic DNA.

Keywords

  • Trial Sequence
  • Polyadenylation Site
  • Internet Resource
  • Simple Repeat
  • Request Form

Content

The GRAIL server is one of the many internet resources for predicting genes in uncharacterized genomic DNA. GRAIL has gene models for five different organisms: human, mouse, Arabidopsis, Drosophila and Escherichia coli. A list of possible exons, their positions, reading frames, and scores is returned after submitting a sequence analysis.

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Reporter's comments

Timeliness

Last updated 12 February 1996.

Best feature

The usefulness of GRAIL information is usually realized when integrated into a gene annotation program. So, there is an option to download the GRAIL results so that they can be utilized by another program. Unfortunately, most of these programs are UNIX-based and most casual users do not have access to them.

Worst feature

Navigating the site is difficult and the output is useless without an external helper program of some kind.

Wish list

Too numerous to list. It appears, however, that the initial GRAIL server has been or will be supplanted by GrailEXP, a more sophisticated gene modeling program that builds on the exon-predicting power of GRAIL by adding homology-based prediction. Homology-based prediction is a very powerful method of identifying genes, especially when expressed sequence tags and protein sequences can be incorporated into the prediction algorithms. At the time of writing, however, it appears that this system is working only for human or mouse sequences. While using a mouse sequence worked quite well; choosing the Arabidopsis option and submitting several trial sequences gave no results at all.

Related websites

There are a number of gene prediction websites, including PROCRUSTES, GeneMark, Genie and GENSCAN.

Table of links

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