ABSTRACT
The uRNADB provides aligned, annotated and phylogenetically ordered sequences of
the uRNAs. At the time of manuscript submission (August 1995) it contained
sequences for U1 (78 sequences), U2 (80), U3 (20), U4 (38), U5 (37) and U6
(46). Additional uRNAs of interest will be available by the time you read this.
The uRNADB, located at The University of Texas Health Science Center at Tyler,
offers phylogenetically-arranged alignments of the uRNAs (currently only the U3 snoRNA and the
spliceosomal snRNAs U1, U2, U4, U5 and U6) and the corresponding annotated
sequences. The uRNADB regularly monitors the appearance of new uRNAs;
therefore, the list of RNAs included into the database is expected to grow;
sequences for U7, U8, U11, U12, U14 and U22 will be incorporated and will be
made available soon.
This first release includes 299 eucaryotic uRNA sequences of U1 to U6 (see Table
1
) identified predominantly by their appearance in the primary sequence databases
GenBank (
1
) and EBI (
2
). For each uRNA category, sequences were aligned using the previously described
rules (
3
). Closely related sequences were aligned first; then each aligned group was
aligned against other groups. Conserved nucleotides were used as landmarks to
align the more variable regions. Elements of secondary structure were
considered last in regions of limited primary structure conservation. The
alignments show the phylogenetically-supported base pairings in upper case, and each RNA helix is given an
arabic numeral (according to conventions used e.g. for ribosomal RNAs, see ref.
4
). In contrast to pairing schemes derived from free energy calculations, these
secondary structure models are minimal and provide phylogenetic evidence for
the existence of each base pair.
Table 1
.
Aligned sequences (u1 to u6) in the uRNADB
The two columns on the left indicate the uRNADB identification and the full
species names of the organisms in phylogenetic order. GenBank accession numbers for aligned uRNAs u1 to u6 are tabulated on the right.
Multiple zeros indicate a sequence that was not accessed through GenBank.
Data are freely available in electronic form through the WWW server of The
University of Texas Health Science Center at Tyler at the URL
http://pegasus.uthct.edu/uRNADB/uRNADB.html. Alignments can be visualized and
downloaded in ASCII-format, as printable PostScript versions (with supported base pairing in
reverse print), and in the ALMA alignment editor format (
5
). The individual uRNA sequences can be obtained in the EMBL format, or by
utilizing direct hypertext links to GenBank (
1
) via the accession numbers. Since some data are presented in tabular form, the
use of an HTML3-capable Web-viewer is recommended.
To obtain the uRNADB by anonymous ftp connect to `diana.uthct.edu' (currently
192.88.11.4), login with name `anonymous' and give your full electronic mail
address as password. A help file explains where to find the data. Hardcopies of
the alignments are available also through written contact or through e-mail to `zwieb{at}jason.uthct.edu', however electronic transfer is more
efficient, and is therefore preferred. Suggestions for improvement of the
database are welcome. Please refer to this article if your research is assisted
by the uRNADB.
I thank Kimberly Chittenden for help with extracting sequences from the GenBank
and EBI databases. This work was assisted by NIH grant GM-49034.
REFERENCES