QGRS Mapper 2 is a second generation software suite that generates information on the composition and distribution of putative Quadruplex forming G-Rich Sequences (QGRS) in nucleotide sequences. QGRS Mapper suite is based on published algorithms for recognition and mapping of putative QGRS, and is unique in that it can map quadruplexes in different parts of the transcribed regions and in the context of RNA processing sites. Like the first version, which was one of the first publicly available tools for mapping such motifs in nucleotide sequences, it is also designed to handle the analysis of pre-mRNA sequences, including that are alternatively processed (alternatively spliced or alternatively polyadenylated).

What is new in QGRS Mapper 2?
The main program has been significantly improved for accuracy, efficiency, and sequence retrieval from NCBI databases. It has several enhanced features, including a "Sequence View" that shows mapped G-quadruplexes in the context of the entire pre-mRNA or mRNA nucleotide sequence. This update makes it possible for the user to work directly with the sequences surrounding the mapped G-quadruplexes. Several new modules that can map QGRS in a variety of sequence formats have also been added to the suite.

Sequence Analysis Tools offered by the QGRS Mapper 2 Suite:

Map QGRS in an mRNA NEW: This module maps G-quadruplexes in the 5'UTR, 3' UTR and CDS of mRNAs. Useful in studying the role of G-quadruplex motifs as cis-acting regulatory elements of the mRNA untranslated regions.

Map QGRS in a pre-mRNA: Maps G-quadruplexes in the Exons and Introns of a pre-mRNA/Genomic sequence in the context of its RNA processing sites. It can handle alternatively processed genes with multiple products.

Map ESEs to QGRS in a pre-mRNA NEW: This module identifies mapped G-quadruplexes that overlap ESEs and can be used to investigate the role of G-quadruplex motifs as Exonix Splicing Enhancers.

Analyze a FASTA/Raw sequence: Analysis of a nucleotide sequence in the FASTA or Raw format.

Batch Analysis Tools:

Analyze a list of mRNAs NEW: Helps map G-quadruplexes in the UTRs and CDS in a batch of mRNAs . Useful with long lists of mRNA accession numbers, e.g. that are generated following microarray analysis.

Analyze a set of FASTA sequences NEW: Batch analysis of several nucleotide sequences in the FASTA format, e.g. a set of promoter or telomeric region sequences.