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Please note that these alignments are rigorous, being based on the identification (as much as possible) of homologous nucleotides on the basis of location in the secondary structure as well as similarity in sequence. In other words, these alignments are closely related to the secondary (and presumably higher-order) structures of the RNAs. These are not the alignments you would get from a 'computer' alignment program.
Bacterial RNA alignments
Contains all of the available (i.e. published or in Genbank) bacterial RNase P RNA sequences with each of the main structure classes aligned, in GenBank format. Type A RNAs are those that resemble E. coli; type B are those that resemble Bacillus & its relatives; type C RNAs are those that appear intermediate between type A and B among the green non-sulfur Bacteria. The secondary structures are described in the Genbank-format files as special text 'sequences'. Updated from Harris, et al., 2001 RNA 7:220.
The following alignment is a catenation of the three above, and so contains all of the bacterial RNase P RNA sequences. Because of the substantial differences in type A and B structures (type C is intermediate), the alignment is a bit 'forced', and is not as clean as the individual type alignments. Updated from Harris, et al., 2001 RNA 7:220.
This alignment is from Christian Massire, from the manuscript Massire, et al., 1998 J Mol Biol 279:773. This is the very nice, rigorous alignment used to build his model for the three-dimensional structure of the RNA.
Archaeal RNA alignment
Contains all of the available archaeal RNase P RNA sequences, both type A and type M, in GenBank format. The secondary structure is described in the Genbank-format file as a special text 'sequence'. Updated from Harris, et al., 2001 RNA 7:220.
Plastid RNA alignment
Contains only 3 sequences at this time. The secondary structure is described in the Genbank-format file as a special text 'sequence'. JWBrown, upublished.
Mitochondrial RNase P RNA alignments
This alignment is taken from Sbisa, et al, 1996 J. Mol. Evol. 43:46-57. Unlike the previous alignments, this is based on maximizing sequence similarity since a convincing secondary structure model is not yet available.
Nuclear RNase P RNA alignments
This alignment is a refined version of Dan Frank's alignment (see below), tuned-up for consistency and specific enough so that secondary structures can be automatically generated from the alignment file. JWBrown, unpublished.
Fungal and vertibrate nuclear RNase P RNA sequence alignment from Frank, et al., 2000 RNA 6:1895. This is the best available comprehensive nuclear RNA alinment, but is not as rigorous as the bacterial and archaeal alignments above.
Yeast nuclear RNase P RNA alignment, updated from Tranguch & Engelke, 1993, JBC 268:14045, with some additional sequences added.
Vertibrate nuclear RNase P RNA alignment, updated from Pitulle, et al, 1998 NAR 26:3333, with some additional sequences added.
These alignments are also taken from Sbisa, et al, 1996 J. Mol. Evol. 43:46-57. Unlike the bacterial & archaeal alignments, these are based on maximizing sequence similarity since a convincing secondary structure model is not yet available.
Please note that these are not rigorous alignments - they are manually 'tweeked' versions of machine-generated (BLAST) alignments, and are therefore based only on maximization of sequence similarity. JWBrown, unpublished.
Bacterial RNase P protein alignment
Eukaryal, archaeal, and mitochondrial alignments are not yet available due to the small number of sequence available so far. Plastid sequences have yet been determined.