Sequence analysis

• AlleleID® tool for bacterial identification. Link only.
• eBio tools collection of open source bioinformatic programs for Mac OS. Review available.
• Geneious - sequence analysis software, sequence database. Review awailable.
• GeneMarker - Genotyping software. Does not run under Windows Vista. Link only.
• IdentiFire from Qiagen. Species identification using pyrosequencing.
• Mutation Surveyor - Tool for identification of mutation by sequence traces. Link only.
• NextGENe - Sequence analysis tool for solid phase sequeincing. Link only.
• pDRAW32 - plasmid drawing program. Review awailable.
• Vector NTI - sequence analysis software, sequence database. Review awailable.

Promoter analysis

• FirstEF - first-exon and promoter prediction program for human DNA.
• Promoter2.0 predicts transcription start sites of vertebrate PolII promoters in DNA sequences. It has been developed as an evolution of simulated transcription factors that interact with sequences in promoter regions. It builds on principles that are common to neural networks and genetic algorithms.
• WWW Promoter Scan. Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences.

Graphics

• Corel Draw- vector graphic editing software. Review awailable.

Freezer management

• Selen Freezer v.1.02 - freezer management database. Review awailable.

DNA methylation related software

• BiQ Analyzer is a software tool for easy visualization and quality control of DNA methylation data from bisulfite sequencing. Link only.
• CpGIF - CpG Island Finder. Web service.
• CpG Island Explorer CpG Island Explorer is aimed at CpG island searching. A specific feature of this program is that a file containing multiple DNA sequences in FASTA or GB format can be processed in one operation.
• CpG Island Searcher. Web service.
• CpGProD - CpG Island Promoter Detection. a program dedicated to the prediction of promoters associated with CpG islands (CGIs) in mammalian genomic sequences.
• DNA Analytics Software from Agilent Technologies. DNA Analytics 4.0 provides an intuitive user interface for visually exploring, detecting, and analyzing CGH, ChIP, and Methylation data in context with the genome of interest.
• EpiDesigner EpiDesigner is a tool for designing quantitative DNA methylation experiments for Sequenom's EpiTYPER technology. Link only.
• EMBOSS CpGPlot/CpGReport/Isochore The function of the program cpgplot is to plot CpG rich areas, and cpgreport to report all CpG rich regions.
• Methyl Primer Express® from Applied Biosystems - free software for methylation mapping experiments.
• MethPrimer is a program for designing bisulfite-conversion-based Methylation PCR Primers. Currently, it can design primers for two types of bisulfite PCR: 1) Methylation-Specific PCR (MSP) and 2) Bisulfite-Sequencing PCR (BSP) or Bisulfite-Restriction PCR.
• MethTools a toolbox to visualize and analyze DNA methylation data.
• Pyro Q-CpG from QIAGEN quantification of DNA methylation using pyrosequencing. Link only.

Flow cytometry

• FCS Express (link only)
• FlowJo (link only)
• WinList (link only)
• WinMDI

Gel Imaging and analysis

• JelMaker - Gel imaging and analysis software. Link only.

Microarrays

• Array Designer Oligo & cDNA Microarray Design Software. Link only.

References

• Reference manager
• EndNote

Utilities

• Allway Sync- data syncronization software. Review awailable.