RADAR

RNA Data Analysis and Research

[Home] [Structure Alignment] [Constrained Structure Alignment] [Multiple Structure Alignment] [Database Search] [Other Features]

Constrained alignment is a powerful feature that allows RNA secondary structure alignment to be carried out dynamically based on prior knowledge about the RNA molecule or special requirements of the user. This function improves the performance of database search by making the search results more specific to the purpose. The constrained region is annotated in the query with "*".

Query:

Sample RNA structure

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Subject:

Sample RNA structure dataset

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>NM_000032:1-52 Homo sapiens aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia) (ALAS2), nuclear gene encoding mitochondrial protein, mRNA CACCUGUCAUUCGUUCGUCCUCAGUGCAGGGCAACAGGACUUUAGGUUCAAG .(((((...((((((.(((((......)))))))).)))...)))))..... >NM_014585:1-100 Homo sapiens solute carrier family 40 (iron-regulated transporter), member 1 (SLC40A1), mRNA AGCGGGACGCCCGGGCGGCCCUGAAGGGGACGGGGCGGCCCCAGUCGGAGGUCGCAGGGAGCUCCGCCCCCGACUCGGUAUAAGAGCUGGGCCCGGCCCA ...(((..((((((((.((((((.......)))))).)))).((((((.((.((.((....)).)))).)))))).............))))....))). >NM_002081:51-150 Homo sapiens glypican 1 (GPC1), mRNA CGCCGCCGCCGGCUUUUGUUGUCUCCGCCUCCUCGGCCGCCGCCGCCUCUGGACCGCGAGCCGCGCGCGCCGGGACCUUGGCUCUGCCCUUCGCGGGCGG .((((....)))).............((((((.(((.((((((.(.(((........)))).))).)))))))))....))).((((((.....)))))) >NM_003449:1001-1100 Homo sapiens tripartite motif-containing 26 (TRIM26), mRNA GGCAGUACAUUGUGGCUGAGUUUGAGCAGGGUCAUCAGUUCCUGAGGGAGCGGGAGGAACACCUGCUGGAACAGCUGGCGAAGCUGGAGCAGGAGCUCAC ..((((...((((((((..((((.((((((.((.((.(((((....)))))..)).))...)))))).))))))))).))).))))((((....)))).. >NM_018992:451-550 Homo sapiens potassium channel tetramerisation domain containing 5 (KCTD5), mRNA CAUUAAUAAAACUUGUAAAGGACAAAAUUAGAGAACGAGACAGCAAAACAUCGCAGGUGCCUGUGAAGCAUGUGUACCGUGUGCUGCAGUGCCAGGAGGA ((((.......(((((..................))))).((((......((((((....)))))).(((((.....))))))))).))))((....)). >NM_014585:151-250 Homo sapiens solute carrier family 40 (iron-regulated transporter), member 1 (SLC40A1), mRNA UCGGACGACCUGCUGAGCCUCCCAAACCGCUUCCAUAAGGCUUUGCCUUUCCAACUUCAGCUACAGUGUUAGCUAAGUUUGGAAAGAAGGAAAAAAGAAA ........(((((.((((((.................)))))).))(((((((((((.(((((......)))))))).)))))))).))).......... >NM_000146:1-100 Homo sapiens ferritin, light polypeptide (FTL), mRNA GUCCCGCGGGUCUGUCUCUUGCUUCAACAGUGUUUGGACGGAACAGAUCCGGGGACUCUCUUCCAGCCUCCGACCGCCCUCCGAUUUCCUCUCCGCUUGC (((((.(((((((((.((.((.(((((......)))))))))))))))))))))))............................................

Gap penalty (default -2)

Alignment type Global Local

Score matrix

>single-base scoring matrix: A C G U A 1 -1 -1 -1 C -1 1 -1 -1 G -1 -1 1 -1 U -1 -1 -1 1 >base-pair scoring matrix: AU CG GC GU UA UG AU 3 1 1 1 1 1 CG 1 3 1 1 1 1 GC 1 1 3 1 1 1 GU 1 1 1 3 1 1 UA 1 1 1 1 3 1 UG 1 1 1 1 1 3

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