Resources

We have been involved in making web servers, software and databases for applications in bioinformatics.

Webservers (and accompanying software)

The webservers include prediction servers as well as various tools for biological sequence analysis. The corresponding software packages are also available for many of the web pages listed below.

	FOLDALIGN 2.0 - Pairwise local structural alignment of RNA sequences. FOLDALIGN (1.0) Local structural alignment of RNA sequences. SLASH - Stem-Loop Align SearcH. Combining FOLDALIGN and COVE.
	The RK Page - Computing the K category correlation coefficient.
	rnadbtool - Semi-automated update and cleanup of structural RNA databases.
	MatrixPlot - Visualize sequence and structure constraints.
	distanceP - Protein distance constraint predictions.
	RNA Structure Logos - Visualize the information content of DNA and RNA sequence and structure alignment.
	Protein Logos - Visualize the information content of protein sequence alignments.
	CPHmodels 1.0 - Protein structure from sequence using protein distance constraint predictions.

Software only

Packages with software and documentation only.

SARSE - Semi-Automated RNA Sequence Editor.

Databases

	PigEST - Porcine EST assembly, expression and SNP data. PigEST more: PigESTncRNA: Non-coding RNAs in PigEST. PigEST genomemap: Genomic mappings of PigESTs. PigESTmito: Porcine mitochondria of PigEST. Expression and SNPs.
	piggenome.dk - Genomic sequences from the Sino-Danish pig genome project. pig micro satelites.
	NEW cmf_encode - Database of CMfinder predicted conserved RNA structures in the ENCODE regions. Many regions are re-aligned using RNA structure constraints.
	hm_ncrna_scan - Database of predicted conserved RNA structures in corresponding region between human and mouse unalignable in primary sequence.
	SRPDB - Signal recognition particle database (local mirror). Includes structural alignment of the SRP RNA sequences.
	tmRDB - tmRNP Database (local mirror). Includes structural alignment of tmRNA sequences.
	telomDB - Telomerase Database (local mirror).

Miscellaneous

	column format - An easy to parse and flexible format for structural alignments.
	Micro RNA in silico methods