Analysis Software

The GESTALT Workbench

Large amounts of 'raw' genomic sequence data already exist and continue to grow exponentially. Many tools are available for automated analysis of these data by comparison to known sequences or by pattern recognition. One of the hardest problems is how to present the sequence data and its derived annotation in an intuitive way. We present here a workbench for analysis of large-scale genomic sequence data, with strong emphasis on the production of enriched graphical representation of the analysed data. The GESTALT Workbench can execute a variety of external analysis programmes (e.g.

BioTapestry

BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks.

Kaviar (queryable database of known variants)

(~Known VARiants) is a very simple tool for answering a very specific question:
What variants have been reported already for a given specific genomic location?

Tags: 

PeptideSieve

It has been noted [1] that only a handful of a protein’s possible tryptic peptides are consistently observed in proteomics experiments. We denote these consistently observed peptides to be proteotypic peptides. Such peptides have a variety of potential applications in proteomic research including improving protein identification scoring functions of database search software, providing a panel of reagents for protein quantification as well as the annotation of genomes for coding sequences of e.g.

Corra

Corra is a single, user-friendly, informatic framework, that is simple to use and fully customizable, for the enabling of LC-MS-based quantitative proteomic workflows of any size, able to guide the user seamlessly from MS data generation, through data processing, visualization, and statistical analysis steps, to the identification of differentially abundant or expressed candidate features for prioritized targeted identification by subsequent MS/MS.

ATAQS (Automated and Targeted Analysis with Quantitative SRM)

As a complement to the well-established discovery proteomic methods, targeted mass spectrometry based on SRM is becoming an important tool for the generation of reproducible, sensitive and quantitatively accurate data from biological samples.

BioSap (Blast Integrated Oligonucleotide Selection Accelerator Package)

The advent of custom designed oligonucleotide microarrays made possible by recent advancements in ink-jet microarray synthesis technology, provides the opportunity to quickly iterate through different microarray experiments. This necessitates designing oligonucleotides quickly, effectively, and by using previously gathered information for more optimal design. The BIOSAP project provides the opportunity to design thousands of oligonucleotides to a given set of biological DNA sequences.

Libra

Libra is a module within the trans-proteomic pipeline to perform quantification on MS/MS spectra that have isobaric multi-reagent labeled peptides. More specifically, at ISB we use Libra on MS/MS spectra of iTRAQ labeled samples; it can also be used on TMT labeled samples. There is no limitation to the number of channels that Libra can quantitate against.

Pages