DATA ANALYSIS
Microarray data
The core provides access to the Arrayassist software package (underline & link to www.stratagene.com/manuals/ArrayAssist.pdf) from Stratagene. This is an updated version of the Genetraffic software package, performing comparable analyses.
Single gene DNA analysis
The core provides access to the DS Gene software package from Accelrys. This can be used to annotate DNA sequences, perform restriction mapping and identify oligonucleotide primers as well as to predict protein sequence and properties.
Genomic scale analyses
With a constantly growing repertoire of annotated genome sequences, it is now feasible to generate sophisticated and highly informative datasets from whole genome comparisons in silico. Such comparisons have been successfully used to identify regulatory sequence associated with specific genes, and have also identified novel regulatory sequence located in gene-poor regions of the genome. For analyses of this scale, we recommend the following resources, all of which are made freely available to academic users. Use of some services may require generating a free account:
NCBI
MGI
Current mouse gene nomenclature with information on gene expression, phenotypes of genetically modified mice and links to available mouse mutants. This is a very useful portal from which to access many other services.
Ensembl
Browser for annotated whole genome sequences from a variety of species. Single genes or segments of chromosomes can be downloaded with annotation.
Match
Web based service that scans for matches to the Transfac database of transcription factor binding sites within a user-defined query sequence. Multiple parameters can be adjusted in this interface to increase or decrease stringency of matching.
VISTA and rVISTA
Tools for cross-species comparisons of genomic sequences. This site also contains pre-computed alignments of whole genomes in which overrepresentation of transcription factor binding sites can be identified within a group of genes, for example genes coregulated in a microarray analysis.
TraFaC
Tools for identifying transcription factor binding sites across the whole genome. For example, all genes containing a binding motif for a specific transcription factor within a defined distance from the promoter can be identified. Parameters can be modified to search only regions surrounding the promoter or the entire gene. Furthermore, combinations of transcription factor binding sites can be identified.
Cartwheel
Tools for very high-resolution comparison of genomic sequence. These require running Javascript program locally and accessing the Cartwheel server at Caltech.
