Gene Prediction

Gene prediction is for the prediction and determining the coding and non-coding regions present in the given stretches of the sequence. For this, several gene prediction tools are used. 

1) GENSCAN: 

This tool can identify introns, exons, promoter sites and polyA signals. There are other gene prediction tools which do the same. It depends on what the user terms a "Probabilistic Model" of genome sequence composition and gene structure. 

2) GRAIL: 

It stands for Gene Recognition and Analysis Internet Link. GRAIL 1 makes use of a neural network method to recognize coding potential in a fixed length. GRAIL 1a expands on this method by considering regions immediately adjacent to coding regions. 

3) FGENEH/FGENES: 

FGENEH makes use of linear discriminant analysis which predicts the internal exons by looking for structural features such as donor and acceptor splices. 

FGENES can be used when multiple genes are expected to in a given DNA sequences. 

4) GeneID: 

It is used for the examining the putative exons present in the given query sequence based on rule-based system. It assembles those exons into the "most likely a gene" for that given sequence. 

5) HMMgene:

using Hidden Markov Model, it predicts whole genes in any given DNA sequence. It is also used for the alternative predictions of the same sequence. 

There are several other gene prediction tools such as GeneParser, "Michael Zhang's Exon Finder" and PROCRUSTES.