Koetschan et al. (2010) NAR 38:D275-9
Selig et al. (2008) NAR 36:D377-380.
Schultz et al. (2006) NAR 34:W704-7.
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ITS2 3D structure
(Keller et al. 2010)


Chlorophyta hypertree

(Buchheim et al. 2011)
Fig1, Fig2, Fig3, Fig4
Example 1: 5S rRNA
Example 2: ITS2 variant
Example 3: 5.8S rRNA
Example 4: Suboptimal Structures
Example 5: Multiple Templates
Example 6: Templates by GI/Acc number

Custom modeling

Template

Enter one or multiple GenBank Identifier or Accession Number(s) from the ITS2 database: (whitespace separated)


or insert your ITS2 (or any other RNA) sequence(s) and structure(s) in extended FASTA format with structure(s) here*:

* Template structures can include side branches.

Target Sequence(s)

FASTA sequence(s) without structure:

Options

Use matrix

transfer helices (side branches included) with % similarity

Gap costs: gap open gap extension

(Note: Computing time increases linearly with number of sequences. For each sequence, computing time increases with template and target sequence length.)

If you use the database please cite.