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PubMed · 8594611

The RNA modification database.

P F Crain·J A McCloskey
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Abstract

The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA and is maintained as an updated version of the initial printed report. Information provided includes: type(s) of RNA in which found and phylogenetic distribution; common chemical names and symbols; Chemical Abstracts registry numbers and index names; chemical structures; initial literature citations for structural characterization or occurrence and chemical synthesis. The data are available through the World Wide Web, anonymous ftp or from the authors in printed form.

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Computer Communication NetworksDatabases, FactualNucleic Acid ConformationRNAJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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P F Crain, J A McCloskey. 1996-01-01. The RNA modification database.. https://doi.org/10.1093/nar%2F24.1.98

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Computerized polymorphic marker identification: experimental validation and a predicted human polymorphism catalog.

A computational system for the prediction of polymorphic loci directly and efficiently from human genomic sequence was developed and verified. A suite of programs, collectively called POMPOUS (polymorphic marker prediction of ubiquitous simple sequences) detects tandem repeats ranging from dinucleotides up to 250 mers, scores them according to predicted level of polymorphism, and designs appropriate flanking primers for PCR amplification. This approach was validated on an approximately 750-kilobase region of human chromosome 3p21.3, involved in lung and breast carcinoma homozygous deletions. Target DNA from 36 paired B lymphoblastoid and lung cancer lines was amplified and allelotyped for 33 loci predicted by POMPOUS to be variable in repeat size. We found that among those 36 predominately Caucasian individuals 22 of the 33 (67%) predicted loci were polymorphic with an average heterozygosity of 0.42. Allele loss in this region was found in 27/36 (75%) of the tumor lines using these markers. POMPOUS provides the genetic researcher with an additional tool for the rapid and efficient identification of polymorphic markers, and through a World Wide Web site, investigators can use POMPOUS to identify polymorphic markers for their research. A catalog of 13,261 potential polymorphic markers and associated primer sets has been created from the analysis of 141,779,504 base pairs of human genomic sequence in GenBank. This data is available on our Web site (pompous.swmed.edu) and will be updated periodically as GenBank is expanded and algorithm accuracy is improved.

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