QGRS-Conserve: a computational method for discovering evolutionarily conserved G-quadruplex motifs.

Background: Nucleic acids containing guanine tracts can form quadruplex structures via non-Watson-Crick base pairing. Formation of G-quadruplexes is associated with the regulation of important biological functions such as transcription, genetic instability, DNA repair, DNA replication, epigenetic mechanisms, regulation of translation, and alternative splicing. G-quadruplexes play important roles in human diseases and are being considered as targets for a variety of therapies.

Development of an undergraduate bioinformatics degree program at a liberal arts college.

The highly interdisciplinary field of bioinformatics has emerged as a powerful modern science. There has been a great demand for undergraduate- and graduate-level trained bioinformaticists in the industry as well in the academia. In order to address the needs for trained bioinformaticists, its curriculum must be offered at the undergraduate level, especially at four-year colleges, where a majority of the United States gets its education.

QGRS-H Predictor: a web server for predicting homologous quadruplex forming G-rich sequence motifs in nucleotide sequences.

Naturally occurring G-quadruplex structural motifs, formed by guanine-rich nucleic acids, have been reported in telomeric, promoter and transcribed regions of mammalian genomes. G-quadruplex structures have received significant attention because of growing evidence for their role in important biological processes, human disease and as therapeutic targets. Lately, there has been much interest in the potential roles of RNA G-quadruplexes as cis-regulatory elements of post-transcriptional gene expression.

Bioinformatics approaches for studying untranslated regions of mRNAs.

Interactions between RNA-binding proteins and cis-acting elements in the 5'- and 3'-untranslated regions (UTRs) of transcripts are responsible for regulating essential biological activities, such as mRNA localization, mRNA turnover, and translation efficiency. This chapter introduces some of the publicly available free bioinformatics resources, including software tools and databases, which can be used for predicting, mapping, and characterizing regulatory motifs found in the eukaryotic mRNA-untranslated regions.

GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs.

G-quadruplex motifs in the RNA play significant roles in key cellular processes and human disease. While sequences capable of forming G-quadruplexes in the pre-mRNA are involved in regulation of polyadenylation and splicing events in mammalian transcripts, the G-quadruplex motifs in the UTRs may help regulate mRNA expression. GRSDB2 is a second-generation database containing information on the composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in approximately 29 000 eukaryotic pre-mRNA sequences, many of which are alternatively processed.

QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences.

The quadruplex structures formed by guanine-rich nucleic acid sequences have received significant attention recently because of growing evidence for their role in important biological processes and as therapeutic targets. G-quadruplex DNA has been suggested to regulate DNA replication and may control cellular proliferation. Sequences capable of forming G-quadruplexes in the RNA have been shown to play significant roles in regulation of polyadenylation and splicing events in mammalian transcripts.

Downstream sequence elements with different affinities for the hnRNP H/H' protein influence the processing efficiency of mammalian polyadenylation signals.

Auxiliary factors likely play an important role in determining the polyadenylation efficiency of mammalian pre-mRNAs. We previously identified an auxiliary factor, hnRNP H/H', which stimulates 3'-end processing through an interaction with sequences downstream of the core elements of the SV40 late polyadenylation signal. Using in vitro reconstitution assays we have demonstrated that hnRNP H/H' can stimulate processing of two additional model polyadenylation signals by binding at similar relative downstream locations but with significantly different affinities.