Bioinformatics
With the increasing demand for high throughput technology in biological studies at EMBL the requirement for bioinformatics supporting GeneCore's users has greatly increased. Starting with microarray analysis it has been necessary to offer guidance about the best ways to analyze data produced and this has increased massively with the incorporation of Next Generation Sequencing in GeneCore's portfolio of services. We deal with the ever increasing amount of data produced and are working to enhance the output of the sequencer giving the best data yields possible.
At GeneCore we provide the following Bioinformatics Support
- Assistance with experimental design of high throughput studies, such as required samples and replicates.
- Guidance on analytical techniques to orientate our users in the world of high throughput data analysis.
- Custom software development of analytical tools such as the MiChip Bioconductor library for the MiChip miRNA microarray platform.
- Providing commercial software to the user base such as the Genomatix package as a biologist user friendly package for NGS data analysis.
- In certain cases data analysis on a collaborative basis.
As well as using and contributing open source projects such as Bioconductor (www.bioconductor.org), we also maintain a number of commercial products for our users.
Genomatix Software
GeneCore has a site wide license for using the Genomatix software package. The software consists of a set of web based tools for analyzing experiments built over an extensive proprietary database of gene, promoter and transcription factor information from 21 species. This software provides a user friendly environment to the analysis Next Generation sequencing data as well as a platform for promoter and transcription factor analysis.
Analyzing Next Generation Sequencing Data with Genomatix RegionMiner
RegionMiner from the Genomatix provides the user with an easy way to analyse their ChipSeq and RNASeq data. Alignment data in BED file format is loaded into the system. From there aligned reads can be clustered into peaks using a variety of methods and the number of peaks in various regions is produced.
Summary data including chromosome and exon/intron read distribution which can be used to assess the success of the experiment is produced as well as bed files containing peak positions and sequences which can be used in downstream analyses. Here the combination of the user friendly interface and the database make comparison of the peak positions with genomic features such as transcription start sites very easy.
In addition to the above the RNASeq analysis produces a spreadsheet of normalized expression values per annotated transcript per gene (method published in Sultan et al Science 15 August 2008:).
Once the peaks have been called regardless of RNASeq or ChipSeq the large database of gene annotation named ElDorado can be combined with the peak call and read data browse the genome at low level with the integrated genome browser. This allows aligning of peaks with genes and their various experimentally annotated and predicted promoters.
Promoter Analysis with Genomatix
The Genomatix software grew out of promoter and transcription factor analysis expertise which is evident in the database containing extensive promoter annotation and transcription factor binding site predictions. This database can be used to search for known transcription factor binding motifs, in specific regions of one or many gene promoters. To look for combinations of transcription factors forming modules (specific combinations of binding sites) or to compare regions looking for cross species homology. This can be done with lists of genes obtain from whatever source be it Next Generation Sequencing or Microarray analysis.
GeneCore licensed 10 seats for our users.
Partek Genomics Suite
Partek's Genomics suit which is a analysis software package for genomic applications including all microarray and next generation sequencing technologies, including gene expression, chip-chip, RNA-seq, chip-seq and many more. It's easy to get started with but has modern methods of data analysis integrated and a easy to work with workflow.
There is one license available localy on one of GeneCore's PCs.
Gene Spring GX Software
Gene Spring GX is a statistical tool for visualization and analysis of expression and genomic structural variation data enabling understanding of microarray data within a biological context. The software is provided in collaboration with EMBL ITS.
Please contact IT for installation of a personal copy of the software on your local machine.
DNA Star Lasergene Suite
A package for manipulating Next Generation Sequence data, including aligner, assembler and viewer. One license for Lasergene NGen is at one GeneCore PC.
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