SUMMARY MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequencecomplementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ

The MetaCyc database (MetaCyc.org) is a compre-hensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scien-tific literature

Identifying parental chromosomes and genomic rearrangements in animal hybrid complexes... 287

TIGR has developed, and continues to refine, a comprehensive, efficient system for small genome annotation. The Glimmer gene finding software identifies open reading frames most likely to code for genes. The protein sequences from these genes are searched against a nonredundant protein database

DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human

miRNAs that differ by as little as one nucleotide. Furthermore, they are not affected by genomic DNA contamination. Precise quantification is achieved routinely with as little as 25 pg of total RNA for most miRNAs. In fact, the high sensitivity, specificity and precision of this method allows

The small genome of Arabidopsis contains at least nine expressed P-tubulin (TUB) genes, in contrast to the large genomes of vertebrate animals, which contain a maximum of seven expressed P-tubulin genes. In this study, we report the structures of seven new TUB genes (TUBP, TUB3, TUBB, TUB6, TUB7

We report an efficient method to detect functional RNAs. The approach, which combines comparative sequence analysis and structure prediction, yields excellent results already for a small number of aligned sequences and is suitable for large scale-genomic screens. It consists of two basic components

, which scales up gracefully to large data sets with millions of training samples, and extends naturally to various matrix factorization formulations, making it suitable for a wide range of learning problems. A proof of convergence is presented, along with experiments with natural images and genomic data

PROSITE is a compilation of sites and patterns found in protein sequences; it can be used as a method of determining the function of uncharacterized proteins translated from genomic or cDNA sequences. In some cases the sequence of an unknown protein is too distantly related to any protein of known