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Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5′ splice site strength

Research Council Cancer Unit, University of Cambridge , Cambridge Biomedical Campus, Box 197, Cambridge CB2 0XZ , UK 1 Vihandha O. Wickramasinghe and Mar Gonzàlez-Porta are joint first authors. John C

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

Background RNA sequencing has opened new avenues for the study of transcriptome composition. Significant evidence has accumulated showing that the human transcriptome contains in excess of a hundred thousand different transcripts. However, it is still not clear to what extent this diversity prevails when considering the relative abundances of different transcripts from the same ...

Temporal dynamics and transcriptional control using single-cell gene expression analysis

Background Changes in environmental conditions lead to expression variation that manifest at the level of gene regulatory networks. Despite a strong understanding of the role noise plays in synthetic biological systems, it remains unclear how propagation of expression heterogeneity in an endogenous regulatory network is distributed and utilized by cells transitioning through a key ...

Vaccinia protein-protein interactions

The availability of the complete sequence of the vaccinia virus genome has enabled a comprehensive two-hybrid analysis in yeast of virus protein-protein interactions.

Making alignments prettier

BoxShade takes sequence alignments and creates an output file in which the alignment is displayed with identical or similar residues shaded in two different tones of gray.

Finding restriction sites

Webcutter provides a free and easy-to-use interface for the analysis of restriction sites in any sequence.

A census of yeast protein-protein interactions

Genome-wide yeast two-hybrid screening has provided a census of protein-protein interactions in Saccharomyces cerevisiae.

Links to molecular biology databases

Finding the relevant database is not always easy, and for some years Nucleic Acids Research has dedicated its first issue of the year to information about the most important existing databases.

Clustering of protein families

Mar Albà RegistrationDate : 1999-12-20 Received : 1999-12-20 OnlineDate : 2000-4-27 - The Protomap program classifies proteins into clusters according to sequence similarity. The Protomap program

Analysis of protein sequences

Several programs to predict sequence and structural features of a protein can be run simultaneously on the PredictProtein server.

Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples

Background A great deal of interest has been generated by systems biology approaches that attempt to develop quantitative, predictive models of cellular processes. However, the starting point for all cellular gene expression, the transcription of RNA, has not been described and measured in a population of living cells. Results Here we present a simple model for transcript levels ...

Mutation patterns of amino acid tandem repeats in the human proteome

Background Amino acid tandem repeats are found in nearly one-fifth of human proteins. Abnormal expansion of these regions is associated with several human disorders. To gain further insight into the mutational mechanisms that operate in this type of sequence, we have analyzed a large number of mutation variants derived from human expressed sequence tags (ESTs). Results We ...

Replicative DNA polymerases

Summary Replicative DNA polymerases are essential for the replication of the genomes of all living organisms. On the basis of sequence similarities they can be classified into three types. Type A polymerases are homologous to bacterial polymerases I, Type B comprises archaebacterial DNA polymerases and eukaryotic DNA polymerase α, and the bacterial polymerase III class make up type ...

Housekeeping genes tend to show reduced upstream sequence conservation

Background Understanding the constraints that operate in mammalian gene promoter sequences is of key importance to understand the evolution of gene regulatory networks. The level of promoter conservation varies greatly across orthologous genes, denoting differences in the strength of the evolutionary constraints. Here we test the hypothesis that the number of tissues in which a ...

Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes

Background Model organisms have contributed substantially to our understanding of the etiology of human disease as well as having assisted with the development of new treatment modalities. The availability of the human, mouse and, most recently, the rat genome sequences now permit the comprehensive investigation of the rodent orthologs of genes associated with human disease. Here, ...