Bioinformatics Tools

A classified list of Bioinformatics tools for RNA analysis.

Structure Prediction — by admin — last modified 2006-10-27 22:25

Great number of softwares have been dedicated to this category but still secondary structure prediction is a hard problem. Traditional softwares such as mfold and RNAfold use dynamic programming based on free energy minimization. Recent methods incorporate multiple sequence alignment into secondary structure prediction, which greatly helps eliminating unconserved structure.

Alignment — by admin — last modified 2006-10-27 22:25

Aligning RNA sequences is computationaly expensive when only nucleotide sequences are given but their secondary structures are not given. Because we would like to estimate an optimal alignment and an optimal common secondary structure in a same time. Sankoff's algorithm has been known as a solution to this problem since very early era of Bioinformatics. However, it is only too expensive algorithm to compute even on today's computers. Many new algorithms are developed in this category.

Gene Finder — by admin — last modified 2006-10-27 22:25

There is no real RNA gene finder as we know it for protein-coding genes. The first ambitious attempt was made by E. Rivas and S.R. Eddy with NCRNASCAN. Unfortunately, RNA genes are quite different from protein-coding genes. There is no golden rule like codon usage of protein-coding genes for RNA genes. However, QRNA and RNAz proposed totally new approach to solve this problem.

Motif Finder — by admin — last modified 2006-10-27 22:25

Motif finders are tools to find the most conserved secondary structure patters in a set of un-aligned nucleic acids sequences.

siRNA — by Mituyama Toutai — last modified 2007-01-31 23:02

Tools for siRNA sequence design

Visualizer — by admin — last modified 2006-10-27 22:25