cDNA2Genome: a tool for mapping and annotating cDNAs.
BACKGROUND
In the last years several high-throughput cDNA sequencing projects have been funded worldwide with the aim of identifying and characterizing the structure of complete novel human transcripts. However some of these cDNAs are error prone due to frameshifts and stop codon errors caused by low sequence quality, or to cloning of truncated inserts, among other reasons. Therefore, accurate CDS prediction from these sequences first require the identification of potentially problematic cDNAs in order to speed up the posterior annotation process.


RESULTS
cDNA2Genome is an application for the automatic high-throughput mapping and characterization of cDNAs. It utilizes current annotation data and the most up to date databases, especially in the case of ESTs and mRNAs in conjunction with a vast number of approaches to gene prediction in order to perform a comprehensive assessment of the cDNA exon-intron structure. The final result of cDNA2Genome is an XML file containing all relevant information obtained in the process. This XML output can easily be used for further analysis such us program pipelines, or the integration of results into databases. The web interface to cDNA2Genome also presents this data in HTML, where the annotation is additionally shown in a graphical form. cDNA2Genome has been implemented under the W3H task framework which allows the combination of bioinformatics tools in tailor-made analysis task flows as well as the sequential or parallel computation of many sequences for large-scale analysis.


CONCLUSIONS
cDNA2Genome represents a new versatile and easily extensible approach to the automated mapping and annotation of human cDNAs. The underlying approach allows sequential or parallel computation of sequences for high-throughput analysis of cDNAs.
Del Val
Coral
C
Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany. c.delval@dkfz.de
Glatting
Karl-Heinz
KH
Suhai
Sandor
S
D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics* / Q000502:physiology; D030541:Databases, Genetic; D005091:Exons / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D020407:Internet; D007438:Introns / Q000235:genetics; D011237:Predictive Value of Tests; D016415:Sequence Alignment / Q000379:methods / Q000592:standards; D012984:Software; D012985:Software Design; D013997:Time Factors
D018076:DNA, Complementary; D004247:DNA