Biomedical subjects

Todd E Scheetz

Publications and source records attributed to Todd E Scheetz.

3 recordsLinked to original sources

PubMed2003

ESTprep: preprocessing cDNA sequence reads.

MOTIVATION: High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases. RESULTS: This paper describes ESTprep, a program designed to preprocess expressed sequence tag (EST) sequences. It identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. Use of ESTprep has resulted in substantial improvement in accurate EST feature identification and fidelity of results submitted to GenBank. AVAILABILITY: The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html

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PubMed2002

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.

The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene. ESTs were generated from libraries enriched for full-length cDNAs and analyzed to identify candidate full-ORF clones, which then were sequenced to high accuracy. The MGC has currently sequenced and verified the full ORF for a nonredundant set of >9,000 human and >6,000 mouse genes. Candidate full-ORF clones for an additional 7,800 human and 3,500 mouse genes also have been identified. All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:mgc.nci.nih.gov).

Algorithms↗

PubMed2002

Identification and initial characterization of 6,000 expressed sequenced tags (ESTs) from rat normal-growing cartilage and swarm rat chondrosarcoma cDNA libraries.

Chondrosarcoma is the second most common type of skeletal malignancy with a survival rate at five years for histological grade III of only 29 percent. The development of a reliable chondrosarcoma animal model could enable the study of tumor growth and progression, the effect of the host on tumor behavior, and the effectiveness of various therapeutic modalities. The Swarm rat chondrosarcoma is a tumor tissue line that has been maintained through the years by serial subcutaneous injections, and the histochemical characteristics of the tumor have remained essentially similar in all transplants over the years. This study was designed to initiate the characterization of the Swarm rat chondrosarcoma model by gene expression profiling as compared to normal-growing rat cartilage. Analysis of the gene expression from both libraries revealed a complex pattern of gene expression, including many genes not yet reported to be expressed by chondrocytes. It suggests that the biochemical characterization of growing cartilage and chondrosarcoma reported to date has only begun to describe the complexity of these tissues.

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