Database for SSU rRNA secondary structures of Porifera

This database contains secondary structure information for the nuclear encoded Small Subunit  ribosomal RNA (SSU rRNA, 18S rRNA) of Phylum Porifera. The secondary structure information is provided for representative taxa in bracket-dot annotation in *.fasta-format and in a *.ct-like format and can be used for the application of rRNA-specific evolutionary models.

The sequences presented here are provided in the naming scheme: Genus_species_GenBankAccession#.

Note that IDs in NCBI GenBank can change, while the accession# is the constant; sequences included here, are therefore not necessarily presented with a valid species name. Please check e.g. the World Porifera Database if you are unsure about species names.

Because many sequences of SSU rRNA are not complete, missing nucleotides at the beginning or at the end of the fragment is represented by "o". Due to sequencing errors, missing data can also be present within the fragment. No attempt was made to compensate potentially 'mis'-sequenced SSU rRNA molecules by introducing 'missing' data within the fragment.

Data:
   taxonomical:
      Class Calcarea
      Class Demospongiae
      Class Hexactinellida

   alphabetical list
   all as *.fasta-format
  
all in *.ct-like-format  

Perl scripts for file conversion and processing of data are provided here. All scripts are written for Mac OS X and Unix-Systems. Most scripts can be used with files in  SeaView (*.mase)-format or *.fasta-files.

Skeleton-files to visualize the provided *.ct-like structures with RnaViz2 can be downloaded here.