[Bio-www] Analysis of Next Generation Sequencing data

Klaus May via bio-www%40net.bio.net (by may from genomatix.de)
Tue Jul 29 08:17:22 EST 2008

Dear Group members,

a recent Science publication:
"A Global View of Gene Activity and Alternative Splicing by Deep
Sequencing of the Human Transcriptome"

demonstrates capabilities of two products from Genomatix

Genomatix delivers powerful turnkey solutions downstream of Next
Generation Sequencing (NGS) devices, following the Genomatix tradition
of highest scientific standards and cutting edge technology.

Genomatix solutions work with data from all available NGS system
providers: Illumina´s Genome Analyzer (Solexa), Roche (454), The SOLiD
TM System by Applied Biosystems, and HeliScope by Helicos.

Genomatix Mapping Station (GMS) delivers ultra-fast mapping of
sequence reads of any length above 9 base pairs. Ten million typical
NGS reads of variable lengths are perfectly and uniquely mapped to the
human genome in less than 30 minutes. GMS is flexible and allows for
any number of indels and point mutations, delivering an uniqueness
measure for each mapped read. It takes the NGS system internal error
checking into account and detects new SNPs. Cutting edge technology
identifies splice junction tags for advanced transcriptome analysis.

Genomatix Genome Analyzer (GGA) is the complete solution for ChIP-seq
and transcriptome analysis downstream of mapping the NGS system reads
to the genome with the Genomatix Mapping Station, or any other
technology. Terabytes of annotation data complement the results from
the NGS experiment and expand by optional integration with each new
sequencing run to a customized genome database. Easy-to-use
visualization and genome wide correlations allow for meta-analysis of
all kind of data-sets.

Integrated comparative genomics procedures allow for phylogenetical
conservation analysis of findings.

Genome wide transcription factor analysis, gene regulatory region
analysis, regulatory SNPs, epigenetic modification analysis, DNase-
seq, digital gene expression with normalization and quantification of
expression values… all required data and hardware in one technology
unit at your lab. GGA is operated through a comprehensive easy-to-use
web based interface for the biologist, plus features full data
structure access and command line driven procedures for the bio-
informatician for easy integration into own high-throughput pipelines.

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