Gene Prediction Methods in Bioinformatics

Study Notes

Data mining is the extraction of knowledge from large amounts of data, and it is also called Knowledge Discovery in Databases (KDD).
In bioinformatics, data mining helps extract useful knowledge from massive datasets gathered in biology, medicine, and neuroscience.
The two primary goals of data mining are prediction and description, and applications of data mining to bioinformatics include gene finding, protein function detection, and disease diagnosis.
Gene prediction in prokaryotes is less complex than in eukaryotes due to smaller genome size, high gene density, and fewer repeat sequences.
Bacterial genes have the Shine-Dalarno sequence and terminator sequence, making gene prediction easier than in higher eukaryotes.
Gene prediction methods include Intrinsic or ab initio prediction, Extrinsic or evidence-based prediction, and homology-based prediction.
Ab initio prediction is based on the identification and analysis of signals found in protein coding genes, such as start and stop codons, intron splice signals, and transcription factor binding sites.
Extrinsic prediction combines ab initio prediction with extrinsic information, such as matches to protein databases or alignments of genomic sequences.
Homology-based prediction identifies significant matches of the query sequence with sequences in known and annotated genome sequences from related species, based on the molecular evolutionary principle that functionally important parts of the genome evolve at a slower rate compared to the rest of the genome.
Transcription of all classes of RNA in prokaryotes is catalyzed by one RNA polymerase, which is a multi-subunit enzyme consisting of two alpha subunits, one beta subunit, one beta prime subunit, one omega subunit, and one sigma factor.
Sigma factor helps direct the enzyme to the promoter, which has two consensus sequences, one at -10 position (TATAAT) known as Pribnow box, and the other at -35 position (TTGACA) from the transcription starting site.
Examples of gene prediction tools include AUGUSTUS, FGENESH, GENSCAN, and GeMoMa software.

Description

Test your knowledge of gene prediction methods in bioinformatics with this quiz! Learn about data mining in biology, the different types of gene prediction methods, and the unique challenges of gene prediction in prokaryotes and eukaryotes. Discover the role of RNA polymerase and sigma factor in transcription, and familiarize yourself with popular gene prediction tools used in bioinformatics research. Challenge yourself and see how much you know about this fascinating field!