XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis.
BACKGROUND
Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have analyzed 350,468 Xenopus laevis Expressed Sequence Tags (ESTs) both to identify full length protein encoding sequences and to develop a unique database system to support comparative approaches between X. laevis and other model systems.


METHODS
Using a suffix array based clustering approach, we have identified 25,971 clusters and 40,877 singleton sequences. Generation of a consensus sequence for each cluster resulted in 31,353 tentative contig and 4,801 singleton sequences. Using both BLASTX and FASTY comparison to five model organisms and the NR protein database, more than 15,000 sequences are predicted to encode full length proteins and these have been matched to publicly available IMAGE clones when available. Each sequence has been compared to the KOG database and approximately 67% of the sequences have been assigned a putative functional category. Based on sequence homology to mouse and human, putative GO annotations have been determined.


CONCLUSIONS
The results of the analysis have been stored in a publicly available database XenDB http://bibiserv.techfak.uni-bielefeld.de/xendb/. A unique capability of the database is the ability to batch upload cross species queries to identify potential Xenopus homologues and their associated full length clones. Examples are provided including mapping of microarray results and application of 'in silico' analysis. The ability to quickly translate the results of various species into 'Xenopus-centric' information should greatly enhance comparative embryological approaches.
Sczyrba
Alexander
A
AG Praktische Informatik, Technische Fakultät, Universität Bielefeld, D-33594 Bielefeld, Germany. asczyrba@techfak.uni-bielefeld.de
Beckstette
Michael
M
Brivanlou
Ali H
AH
Giegerich
Robert
R
Altmann
Curtis R
CR
D000818:Animals; D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D017931:DNA Primers / Q000737:chemistry; D018076:DNA, Complementary / Q000378:metabolism*; D030541:Databases, Genetic; D030562:Databases, Protein; D004331:Drosophila melanogaster; D020224:Expressed Sequence Tags; D016678:Genome; D006801:Humans; D007091:Image Processing, Computer-Assisted; D020407:Internet; D051379:Mice; D008957:Models, Genetic; D008969:Molecular Sequence Data; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D013045:Species Specificity; D014981:Xenopus; D014982:Xenopus laevis / Q000235:genetics*
D017931:DNA Primers; D018076:DNA, Complementary