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cDNA2Genome: a tool for mapping and annotating cDNAs.

Del Val C, Glatting KH, Suhai S - BMC Bioinformatics (2003)

Bottom Line: 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 underlying approach allows sequential or parallel computation of sequences for high-throughput analysis of cDNAs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany. c.delval@dkfz.de

ABSTRACT

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.

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Screenshot of the web output of cDNA2genome
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Figure 2: Screenshot of the web output of cDNA2genome

Mentions: The final result of cDNA2Genome is an Extensible Markup Language (XML) file which contains all relevant information obtained by the task. This XML output can be used in successive analysis pipelines, or integrated in user databases. At the same time, the web user can easily inspect the XML output through a web browser. The result of cDNA2Genome in the web is summarized in two graphical outputs and one text output (Fig. 2). The text output shows a summary including sequence identifier, description, and scores of the most important hits found for each of the homology searches performed. The first graphical output places the cDNA at its corresponding position in a human chromosome and displays in a comprehensible way the results from each of the homology and database searches and from each of the prediction programs. The second graphical output shows open reading frames (ORFs) in each of the three forward frames with different offsets and colours for each frame. The graphical display provides an interactive graphical view of the annotations (Fig. 2) and is hyperlinked.


cDNA2Genome: a tool for mapping and annotating cDNAs.

Del Val C, Glatting KH, Suhai S - BMC Bioinformatics (2003)

Screenshot of the web output of cDNA2genome
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC239864&req=5

Figure 2: Screenshot of the web output of cDNA2genome
Mentions: The final result of cDNA2Genome is an Extensible Markup Language (XML) file which contains all relevant information obtained by the task. This XML output can be used in successive analysis pipelines, or integrated in user databases. At the same time, the web user can easily inspect the XML output through a web browser. The result of cDNA2Genome in the web is summarized in two graphical outputs and one text output (Fig. 2). The text output shows a summary including sequence identifier, description, and scores of the most important hits found for each of the homology searches performed. The first graphical output places the cDNA at its corresponding position in a human chromosome and displays in a comprehensible way the results from each of the homology and database searches and from each of the prediction programs. The second graphical output shows open reading frames (ORFs) in each of the three forward frames with different offsets and colours for each frame. The graphical display provides an interactive graphical view of the annotations (Fig. 2) and is hyperlinked.

Bottom Line: 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 underlying approach allows sequential or parallel computation of sequences for high-throughput analysis of cDNAs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany. c.delval@dkfz.de

ABSTRACT

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.

Show MeSH