BIOINFORMATICS APPLICATIONS NOTE Databases and ontologies PACdb: PolyA Cleavage Site and 3 ′-UTR Database

UNLABELLED The PolyA Cleavage Site and 3'-UTR Database (PACdb) is a web-accessible database that catalogs putative 3'-processing sites and 3'-UTR sequences for multiple organisms. Sites have been identified primarily via expressed sequence tag-genome alignments, enabling delineation of both the specificities and heterogeneity of 3'-processing events. AVAILABILITY By web browser or CGI: PACdb: http://harlequin.jax.org/pacdb/; AtPACdb: http://harlequin.jax.org/atpacdb/. SUPPLEMENTARY INFORMATION Available online at http://harlequin.jax.org/pacdb/supplemental.php.

[1]  Rithy K. Roth,et al.  Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays , 2000, Nature Biotechnology.

[2]  W. Gish,et al.  Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. , 2001, Genome research.

[3]  Jungwon Yoon,et al.  The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community , 2003, Nucleic Acids Res..

[4]  G. Edwalds-Gilbert,et al.  Alternative poly(A) site selection in complex transcription units: means to an end? , 1997, Nucleic acids research.

[5]  S Audic,et al.  Alternate polyadenylation in human mRNAs: a large-scale analysis by EST clustering. , 1998, Genome research.

[6]  K. Kinzler,et al.  Serial Analysis of Gene Expression , 1995, Science.

[7]  G. Stormo,et al.  Combining SELEX with quantitative assays to rapidly obtain accurate models of protein–DNA interactions , 2005, Nucleic acids research.

[8]  C. MacDonald,et al.  Reexamining the polyadenylation signal: were we wrong about AAUAAA? , 2002, Molecular and Cellular Endocrinology.

[9]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[10]  T. Marr,et al.  Computational analysis of 3'-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat. , 2005, Genome research.

[11]  L. Minvielle-Sebastia,et al.  A comparison of mammalian and yeast pre-mRNA 3'-end processing. , 1997, Current opinion in cell biology.

[12]  Graziano Pesole,et al.  UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs , 2004, Nucleic Acids Res..

[13]  Jing Zhao,et al.  Formation of mRNA 3′ Ends in Eukaryotes: Mechanism, Regulation, and Interrelationships with Other Steps in mRNA Synthesis , 1999, Microbiology and Molecular Biology Reviews.

[14]  D. Gautheret,et al.  Patterns of variant polyadenylation signal usage in human genes. , 2000, Genome research.

[15]  C. Dieckmann,et al.  Regulation of poly(A) site choice of several yeast mRNAs. , 1998, Nucleic acids research.

[16]  Michael Recce,et al.  PolyA_DB: a database for mammalian mRNA polyadenylation , 2004, Nucleic Acids Res..

[17]  Philip Lijnzaad,et al.  The Ensembl genome database project , 2002, Nucleic Acids Res..

[18]  Kara Dolinski,et al.  Saccharomyces genome database: Underlying principles and organisation , 2004, Briefings Bioinform..

[19]  Roy Parker,et al.  Exosome-Mediated Recognition and Degradation of mRNAs Lacking a Termination Codon , 2002, Science.

[20]  T. Marr,et al.  Computational analysis of 3'-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat. , 2005, Genome research.