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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586
These include
* identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads
* prokaryotic sequence/genome annotation
* RNAseq analysis - normalisation and collation of multiple samples as a group
* RNAseq visualisation
All scripts are provided on a 'best efforts' basis, however due to various system changes I do not...
Parallelized calculation of molecular similarities
Diversity assessments and comparisons of large compound databases require calculating similarities of millions of compounds in an affordable time. ParaSim addresses this challenge by parallelizing the calculations according to the number of computing cores available on a single machine. It is optimized for the throughput of very large numbers of query structures against very large numbers of reference structures. As as special feature, ParaSim allows to store and and to access frequently...