Analysis Tools

MIG - The Multi-Image Genome (MIG) viewer
MIG

The Multi-Image Genome viewer (MIG) is primarily aimed at high-throughput sequencing experiments where a "signal" is detected at multiple locations across the genome (such as ChIP-Seq and RNA-Seq). MIG allows the user to filter, sort and visualise these regions of interest in their local genome context.

McGowan SJ, Hughes JR, Han ZP, Taylor S
Bioinformatics (2013) 29: 2477-8
MIG: Multi-Image Genome viewer.

miR-CRISPR
MIG

The miR-CRISPR tool is an integrated algorithm designed to facilitate CRISPR / Cas9 genome engineering of putative microRNA response elements (MREs).

Bassett et al
Nature Communications (2014) 5: 4640
Understanding functional miRNA-target interactions in vivo by site-specific genome engineering.

Zegami
Zegami

Zegami lets you search, sort, filter and group collections of images in real time and in a single field of view. It allows you to load not only your images, but also the associated metadata and has an array of in-built filters that make it easy to see patterns and identify relationships based on the data contained in each image.

Proteomics software
Mascot Server

Mascot Server is a commercial search engine which uses mass spectrometry data to identify proteins from primary sequence databases. The facility shares access to a multi-node Mascot Server cluster hosted by the CBRG.

CPFP

The Central Proteomics Facilities Pipeline (CPFP) allows simultaneous searching and result combination from multiple search engines for statistical analysis of results. It includes tools for quantitative proteomics (LIBRA for iTRAQ/TMT, and ASAP ratio for SILAC) and semi-quantitative label-free analysis (SINQ).

CapSequm
CapSequm

CapSequm is an online tool to design oligonucleotides for multiple targets for use in next generation (NG) Capture-C experiments.

Davies JO, Telenius JM, McGowan SJ, Roberts NA, Taylor S, Higgs DR, Hughes JR
Nature Methods (2015) 13: 74-80
Multiplexed analysis of chromosome conformation at vastly improved sensitivity.

Weapon of Mutant Detection (WMD)
WMD

Weapon of Mutant Detection (WMD) is a bioinformatics tool for the comparison of reference and mutant DNA: identifies restriction enzymes that cut the two sequences in a discriminative manner.

Human Erythroblast Maturation (HEM) Database
CapSequm

The Human Erythroblast Maturation database (HEM) contains differentially regulated and continuously expressed transcripts: a resource for future functional studies of erythropoiesis.

Merryweather-Clarke et al
Blood (2011) 117: e96-108
Global gene expression analysis of human erythroid progenitors.

EMBOSS
EMBOSS

EMBOSS explorer, a graphical user interface to the free, open source bioinformatics analysis package, EMBOSS (" European Molecular Biology Open Software Suite")
Within EMBOSS are more than 100 programs. Some of the areas covered are:

  • Sequence alignment
  • Rapid database searching with sequence patterns
  • Protein motif identification, including domain analysis
  • Nucleotide sequence pattern analysis, for example to identify CpG islands or repeats
  • Codon usage analysis for small genomes
  • Rapid identification of sequence patterns in large scale sequence sets
  • Presentation tools for publication