List of software tools useful for sequencing and fragment analysis. Some software is available in SeqLab's workstations, some you may download freely and install to your computer.

Online primer design - Online genome tools - Chromatogram viewers - Fragment analysis - Sequence analysis

Online primer design

• Primer 3
  • The classic one
• The PCR Suite - modified Primer3
  • Overlapping primers
  • Genomic primers
  • SNP primers
  • cDNA primers
• Multiplex primer designer @GIU
  • Runs on Primer3 engine
• UCSC's BLAT in silico PCR
  • Locate primers in a genome
  • Check specificity of primers
• UCSC's BLAT Search
  • Locate a sequence in a genome
  • Useful in sequencing troubleshooting

• Genome Browsers
  • UCSC Genome Bioinformatics
  • Ensembl Genome Browser
  • NCBI Map Viewer
  • HOWDY Japan
• Variant databases
  • Database of Genomic Variants
    • A curated catalogue of structural variation in the human genome
  • Human Seqmental Duplication Database
    • Segmental duplication data
  • HapMap - haplotype map of the human genome
  • SNPper - retrieve SNP information by flexible queries.Requires (free) registration
  • SeattleSNPs - genotyped SNPs by gene
    • Genome Variation Server
  • dbSNP - a lot of them

• Sequence Scanner v1.0, Applied Biosystems
  • View, edit, print and export raw and analyzed sequence data.
  • Free software
• FinchTV, Geospiza
  • Basic chromatogram viewer for viewing and printing
  • Free software
• Xplorer, dnaTools
  • View, edit, compare chromatograms
  • For sequence and fragment analysis
  • For PC, Mac, Unix
  • Free software
• SeqDoC, University of Queensland
  • Find differences between chromatograms
  • Compare two chromatograms
  • Compare ten chromatograms to a reference
  • Free online service

• PeakScanner, Applied Biosystems
  • For basic DNA fragment analysis
  • Free software
• GeneMapper 4.0, Applied Biosystems
  • Advanced fragment analysis package
  • Requires a licence
  • 2 licences in SeqLab's workstations
• GeneMarker, SoftGenetics
  • Advanced Fragment analysis package
  • Requires a licence
  • 2 licences in SeqLab's workstations
• Xplorer, dnaTools
  • View, edit, compare chromatograms
  • For sequence and fragment analysis
  • For PC, Mac, Unix
  • Free software

• Sequencher 4.7, Genecodes
  • Quick-to-learn sequence analysis tool
• SeqScape 2.5, AppliedBiosystems
  • For large scale resequencing and variant detection
• Mutation Surveyor 3.0, SoftGenetics
  • Resequencing, enhanced InDel detection
• Staden Package, freeware
  • A fully developed set of DNA sequence assembly, editing and analysis tools
• Variant Reporter, Applied Biosystems
  • Resequencing, large scale variant screening