Department of Molecular Biology, The University of Texas Health Science Center at Tyler, Highway 271 N, PO Box 2003, Tyler , TX 75710, USA

Received September 27, 1996; Accepted October 8, 1996

ABSTRACT

The uRNADB offers aligned, annotated and phylogenetically ordered sequences of several U RNAs. New to this release are RNAs from U7 (14 sequences), U8 (two sequences), U11 (three sequences), U12 (two sequences), U14 (11 sequences), U18, U48 and U49. A total of 34 new sequences were aligned with the previously compiled snRNAs U1, U2, U3, U4, U5 and U6.

DESCRIPTION

The uRNADB is located at the University of Texas Health Science Center at Tyler and provides several U RNA sequences in an easily accessible form. Table 1 refers to the sequences that have become available since the previous release ( 1 ), but new U RNAs are added on a regular basis.

For each U RNA (currently U1-U8, U11, U12, U14, U18, U48 and U49) the database shows the sequences in both alphabetical and phylogenetic order. Homologous RNAs are aligned according to the previously described rules ( 2 ), with the RNA helices that are confirmed by comparative sequence analysis indicated in the alignment by arabic numbers ( 3 ). Since only phylogenetically-supported base pairs are included, the determined RNA secondary structure models are minimal, in contrast with structures that are obtained from free energy calculations.

The data are acquired best through the Web 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 directly, or they can be downloaded in ASCII-format, as printable PostScript versions (with supported base pairing in reverse print), and in the ALMA alignment editor format ( 4 ). Individual uRNA sequences are obtained in the EMBL-format directly from the uRNADB, or by using hypertext links to GenBank ( 5 ) or the EBI ( 6 ) via the accession numbers. Data in tables are viewed preferably with an HTML3-capable Web-browser.

Files in the uRNADB can also be accessed by anonymous ftp to `diana.uthct.edu'. (Currently 192.88.11.4; login with name `anonymous' and give your full electronic mail address as the password.) The complete uRNADB can be downloaded from the same site as a compressed `tar-file'. Hardcopies of the alignments are available through written contact or through e-mail to the author at `zwieb{at}jason.uthct.edu'; electronic transfer is preferred. If your research is assisted by the uRNADB please refer to this article and cite the original authors in case you fetch and use data that I only redistribute.

Table 1 . U RNA sequences added to the uRNADB in 1996

snRNA a	ID	Name	Accession b
U1 ( 78 +2)	CAN.SPE.	Canis familiaris	L33345
	TRI.AE-G	Triticum aestivum	X69334
U2 ( 80 +15)	CAN.SPE.	Canis canis	X69482
	HOM.SA-J	Homo sapiens	U57614
	LEP.SEY.	Leptomonas seymouri	U23406
	ORY.SAT.	Oryza sativa	U27085
	TRI.AES.	Triticum aestivum	X69327
	VAI.NEC.	Vairimorpha necatrix	Z50072
U3 ( 20 +5)	EUG.GRA.	Euglena gracilis	U27297
	LEP.CO-A,B	Leptomonas collosoma	L32919, S74819
	SUL.ACE.	Sulfolobus acidocaldarius	U13990
	TRY.CRU.	Trypanosoma cruzi	S74818
U4 ( 38 +1)	LYT.VAR.	Lytechinus variegatus	U37266

Table 1. continued

snRNA a	ID	Name	Accession b
U5 (37+3)	LYT.VAR.	Lytechinus variegatus	U33957
	PHY.PO-A,B	Physarum polycephalum	X74440, X74441
U6 ( 46 +8)	CRI.FA-A,B	Crithidia fasciculata	X78550, X78551
	ENT.HIS.	Entamoeba histolytica	U43841
	LEI.MEX.	Leishmania mexicana	X82228
	LEP.SEY.	Leptomonas seymouri	X78552
	PED.MIN.	Pedinomonas minutissima	U58510
	PHY.SPE.	Phytomonas sp .	X82229
	STR.PUR.	Strongylocentrotus purpuratus	X76546
U7 (13)	CAE.EL-A,B	Caenorhabditis elegans	X15634, X15633
	HOM.SAP.	Homo sapiens	X07185, X07185, X18675
	MUS.MU-A to C	Mus musculus	Z68756
	PSA.MI-A to E	Psammechinus miliaris	M13307, M13308, M13309, M13310, M13311
	XEN.BOR.	Xenopus borealis	Z11688
	XEN.LA-B,C,F	Xenopus laevis	X64404
U8 (2)	RAT.NOR.	Rattus norvegicus	M11057
	XEN.LAE.	Xenopus laevis	L13416
U11 (3)	HOM.SA-A to C	Homo sapiens	X13707
U12 (3)	GAL.GAL.	Gallus gallus	L43844
	HOM.SAP.	Homo sapiens	L43845
	MUS.MUS.	Mus musculus	L43843
U14 (11)	MUS.MU-A,B	Mus musculus	X54402, X54403
	SAC.CER.	Saccharomyces cerevisiae	X96815
	SOL.TUB.	Solanum tuberosum	Z35303
	XEN.LA-A,B	Xenopus laevis	Z49896, Z49897
	ZEA.MA-A to E	Zea mays	Z35298, Z35300, Z35301, Z35302, Z35299
U18 (1)	SAC.CER.	Saccharomyces cerevisiae	U12981
U48 (1)	HOM.SAP.	Homo sapiens	X96648
U49 (1)	HOM.SAP.	Homo sapiens	X96649

^a The first three columns show the U RNA type, the uRNADB identification (ID) and the full species name of the organism, respectively. Bracketed numbers in the first column indicate the number of new U RNA sequences, with italic numbers showing how many sequences were in the previous uRNADB release (1). ^b GenBank (5) and EBI (6) Sequence Retrieval System accession numbers are tabulated on the right.

ACKNOWLEDGEMENTS

I thank Kimberly Chittenden for help with extracting sequences from the GenBank and the EBI databases. This work was assisted by NIH grant GM-49034 to C.Z.

REFERENCES

2 Larsen,N. and Zwieb,C. (1991) Nucleic Acids Res., 19, 209-215.

3 Leffers,H., Kjems,J., Østergaard,L., Larsen,N. and Garrett,R.A. (1987) J. Mol. Biol., 195, 43-61.

4 Thirup,S. and Larsen,N. (1990) Proteins: Struct., Funct. Genet., 7, 291-295.

5 Benson,D.A., Boguski,M., Lipman,D.J. and Ostell,J. (1996) Nucleic Acids Res., 24, 1-5.

6 Rodriguez-Tomé,P., Stoehr,P.J., Cameron,G.N. and Flores,T.P. (1996) Nucleic Acids Res., 24, 6-12.MEDLINE Abstract

Tel: +1 903 877 7689; Fax: +1 903 877 5731; Email: zwieb{at}jason.uthct.edu
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