annotate test-data/segments_truncated.xml @ 2:22d7b6019372 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9

<?xml version="1.0" encoding="UTF-8"?>
<root>
	<segments>
		<segment>
			<id>Kt-CD-box.UGU</id><!-- Common -->
			<sequence_5prime>UGUGAU</sequence_5prime>
			<bonds          >   :::</bonds>
			<sequence_3prime>   AGU</sequence_3prime>
			<energy>-11.1072</energy>
			<directions>
				<five_prime>true</five_prime>
				<three_prime>true</three_prime>
			</directions>
		</segment>
		
		<segment>
			<id>Kt-CD-box.CGU</id><!-- Common -->
			<sequence_5prime>CGUGAU</sequence_5prime>
			<bonds          >   :::</bonds>
			<sequence_3prime>   AGU</sequence_3prime>
			<energy>-11.1072</energy>
			<directions>
				<five_prime>true</five_prime>
				<three_prime>true</three_prime>
			</directions>
		</segment>
	</segments>
	
	
	<segmentloops />
	
	
	<!-- RNA-Molecules -->
	<rnas>
		<rna>
			<title>C/D-box snoRNA</title>
			<organism>A. fulgidus</organism>
			<sequence>GCUCUGACCGAAAGGCGUGAUGAGC</sequence>
			
			<structures>
				<structure>
					<associated_segments>
						<link>Kt-CD-box.CGU</link>
					</associated_segments>
					<dot_bracket type="full"   >(((((((((....))...)))))))</dot_bracket>
				</structure>
				
				<structure>
					<associated_segments />
					<dot_bracket />
				</structure>
			</structures>
			
			<references>
				<pdb>1RLG</pdb>
				<url>http://www.sciencedirect.com/science/article/pii/S0969212604001169</url>
			</references>
		</rna>
		
		<rna>
			<title>Artificial double C/D K-turn construct</title>
			<sequence>GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC</sequence>
			
			<structures>
				<structure>
					<associated_segments>
						<link>Kt-CD-box.UGU</link>
					</associated_segments>
					<dot_bracket type="full"   >((((((((...((((?????????????((((((((((((.....))))))))...))))?????????????))))))))))))</dot_bracket>
				</structure>
				
				<structure>
					<associated_segments />
					<dot_bracket />
				</structure>
			</structures>
			
			<references>
				<pdb>3ICX</pdb>
				<pdb>3ID6</pdb>
				<doi>http://dx.doi.org/10.1038/nature09688</doi>
			</references>
		</rna>
	</rnas>
</root>