XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis

Sczyrba A, Beckstette M, Brivanlou AH, Giegerich R, Altmann CR (2005)
BMC Genomics 6(1).

Download
OA
Journal Article | Published | English
Author
; ; ; ;
Abstract
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. Description: 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 ~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. Conclusion: 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. Supplementary material can be found at http://bibiserv.techfak.uni-bielefeld.de/xendb/.
Publishing Year
ISSN
PUB-ID

Cite this

Sczyrba A, Beckstette M, Brivanlou AH, Giegerich R, Altmann CR. XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics. 2005;6(1).
Sczyrba, A., Beckstette, M., Brivanlou, A. H., Giegerich, R., & Altmann, C. R. (2005). XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics, 6(1).
Sczyrba, A., Beckstette, M., Brivanlou, A. H., Giegerich, R., and Altmann, C. R. (2005). XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics 6.
Sczyrba, A., et al., 2005. XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics, 6(1).
A. Sczyrba, et al., “XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis”, BMC Genomics, vol. 6, 2005.
Sczyrba, A., Beckstette, M., Brivanlou, A.H., Giegerich, R., Altmann, C.R.: XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics. 6, (2005).
Sczyrba, Alexander, Beckstette, Michael, Brivanlou, Ali H., Giegerich, Robert, and Altmann, Curtis R. “XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis”. BMC Genomics 6.1 (2005).
Main File(s)
Access Level
OA Open Access

This data publication is cited in the following publications:
This publication cites the following data publications:

3 Citations in Europe PMC

Data provided by Europe PubMed Central.

Probing the Xenopus laevis inner ear transcriptome for biological function.
Powers TR, Virk SM, Trujillo-Provencio C, Serrano EE., BMC Genomics 13(), 2012
PMID: 22676585
Expression profiles during dedifferentiation in newt lens regeneration revealed by expressed sequence tags.
Maki N, Martinson J, Nishimura O, Tarui H, Meller J, Tsonis PA, Agata K., Mol. Vis. 16(), 2010
PMID: 20090923
IsoSVM--distinguishing isoforms and paralogs on the protein level.
Spitzer M, Lorkowski S, Cullen P, Sczyrba A, Fuellen G., BMC Bioinformatics 7(), 2006
PMID: 16519805

103 References

Data provided by Europe PubMed Central.

Trans-NIH Xenopus Initiative Website
AUTHOR UNKNOWN, 2005
Xenbase Xenopus Web Resource Website
AUTHOR UNKNOWN, 2005

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 16162280
PubMed | Europe PMC

Search this title in

Google Scholar