(95) Multiple RNA-Sequence Alignment Considering Stem Regions

	Machine:     PIM/UNIX Machine
	Environment: PIMOS/UNIX, KLIC
	Language:    KL1
	Source Code: 0.3 MB
	Documents:   Manual (English / Japanese)

Overview

This system refines a rough alignment using a parallel simulated annealing algorithm taking into account connected base pairs in RNA stem regions.

Features

In general, the sum-of-pair alignment does not show complete alignment in terms of stem structures, but merely indicates some possible stem regions. This system refines the rough alignment with a temperature parallel simulated annealing algorithm which optimizes the score obtained by connected base pairs and covariance matches. This procedure gives us a proper RNA-sequence alignment, from which we can specify stem regions.

Function

After a twelve-hour annealing process beginning with a rough alignment done by a parallel iterative algorithm (IFS No.75), this system generated the final RNA alignment as shown below. The alignment identified well-known tRNA stem sets of clover shape. It is important when specifying stem regions correctly to take into account the covariance mutations when aligning RNA sequences, because most stem regions include many such mutations.

This system can also execute on computers with basic functions of UNIX operating system using KLIC.

FTP

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