Gene Prediction Methods and Protocols

Ghovvati, Shahrokh; Golpasand, Sare

doi:10.22124/psug.2025.27208.1066

Gene Prediction Methods and Protocols

Document Type : Translation

Authors

Shahrokh Ghovvati ¹
Sare Golpasand ²

¹ Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, Guilan, Iran.

² Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht, Guilan, Iran.

10.22124/psug.2025.27208.1066

Abstract

Noncoding RNA research is already a routine in every genomics or transcriptomics initiatives.
According to their functions, ncRNAs can be grouped into several different RNA families, which can be
represented by conserved primary sequences, secondary structures, or covariance models. CMs are
very sensitive in predicting RNA families in nucleotide sequences and have been widely used in characterizing
the repertoire of ncRNAs in organisms from all domains of life. However, the large-scale prediction and
annotation of ncRNAs require multiple tools along the process, imposing a great obstacle for researchers
with lesser computational or bioinformatics background. StructRNAfinder emerged as an automated tool
to avoid these bottlenecks, by performing the automatic identification and complete annotation of regulatory
RNA families derived directly from nucleotide sequences. In this chapter, we provide a complete
tutorial for both stand-alone and web server versions of StructRNAfinder. This will help users to install the
tool and to perform predictions of RNA families in any genome or transcriptome sequences dataset.

Graphical Abstract