ESTScan

The ESTScan project is a remarkable software designed to detect coding regions in DNA sequences, even if they are of low quality. This program boasts of the ability to detect and correct sequencing errors that lead to frameshifts, which significantly improves the quality of the results obtained from using ESTScan. It is essential to note that ESTScan is not a gene prediction program; neither is it an open reading frame detector.

Remarkably, the program's strength lies in the fact that it does not require an open reading frame to detect a coding region. This makes ESTScan stand out from other similar software solutions. While it may miss a few translated amino acids at either the N or the C terminus, ESTScan detects coding regions with high selectivity and sensitivity.

ESTScan employs a unique method where it takes advantage of the bias in hexanucleotide usage found in coding regions relative to non-coding regions. The bias is formalized as an inhomogeneous 3-periodic fifth-order Hidden Markov Model (HMM). The HMM of ESTScan has been further extended to allow insertions and deletions when they improve the coding region statistics, which significantly improves the accuracy of the results obtained from using ESTScan.

Overall, ESTScan is an excellent software solution for detecting coding regions in DNA sequences, especially in low-quality sequences. Its unique approach sets it apart from other gene prediction software solutions available in the market, making it a must-have in every researcher's toolbox.