Our Favorite Tools

These are just a few of our favorite software packages. Please let us know if you have a favorite tool that is not listed here.

Chromotogram Viewers

For Windows and Mac OS Windows Specific
  • Chromas, Windows specific chromatogram viewer
  • BioEdit, a sequence alignment viewer and editor
Mac OS Specific

Primer Design

  • Primer3, online primer design on DNA template
  • PrimerX, automated design of mutagenic primers for site-directed mutagenesis based on DNA or protein sequence


Other Tools

Frequently Asked Questions

How should I submit samples?
Should I resuspend my samples in water?
What strains of E coli should I use?
What tips do you have for designing primers?

How should I submit samples?

Type Mixed? Preparation
Plasmid Premixed 0.5ug plasmid DNA + 3pmol primer in 12ul dH2O
Unmixed 0.5ug plasmid DNA in 10ul dH2O
PCR Premixed 100ng/1000bp purified PCR product + 1pmol primer in 12ul dH2O
Unmixed 100ng/1000bp unpurified PCR product in 10ul dH2O

You can find detailed information on the Sample Preparation page.

Should I resuspend my samples in water?

Avoid EDTA in submitted template or primer solutions. We strongly recommend to resuspend template or primer in 10 mM Tris (pH 8.5) or water.

How do I prepare plasmids for sequencing?

  • Plasmid DNAs purified through most commercial kits are suitable for DNA sequencing. Please consult your special supplier for further information.
  • Low copy number plasmids need to be further concentrated before sequencing. These plasmid can be concentrated by ETOH precipitation, centricon spin column, or use our template amplification service (RCA).

You can find detailed information on the Sample Preparation page.

What strains of E coli should I use?

  • E.coli strains can be shipped as single colonies on agar plates. Please use endA- strains such as Dh4α, HB101, and XL1-Blue. The agar should not be too liquid for shipment.

What tips do you have for designing primers?

  • Primer Length: 20-25 bases
  • Base composition: about 50% GC
  • Avoid secondary structures: hairpins, palindromic sequence, dimers, and more 3Gs or 3Cs in a stretch
  • Avoid multiple binding sites on the template: putative binding sites are defined as 80% of your primer sequence or 100% of last 7 bases on the 3' end aligned to another site on the template.
  • The 1st readable base starts about 50 bases downstream of the primer binding site.

Available Common Primers (Complete List in Excel)

Name Description Sequence
3'AOX1 For Pichia vectors with AOX1 terminator, reverse primer GCAAATGGCATTCTGACATCC
5'AOX1 For Pichia vectors with AOX1 promoter, forward primer GACTGGTCCAATTGACAAGC
Alpha-factor Alpha factor signal sequence, forward primer TACTATTGCCAGCATTGCTGC
Amp-R 5' end of ampiciltrn resistance gene, reverse primer ATAATACCGCGCCACATAGC
CAT-R 5' end of chloramphenicol resistance gene, reverse primer GCAACTGACTGAAATGCCTC
CMV Forward Human CMV immediate early promoter, forward primer CGCAAATGGGCGGTAGGCGTG
CRE-R 5' end of Cre recombinase, reverse primer GCAAACGGACAGAAGCATTT
EF-1a Forward Human elongation factor-1a promoter, forward primer TCAAGCCTCAGACAGTGGTTC
GAL1 S. cerevisiae GAL1 promoter, forward primer AATATACCTCTATACTTTAACGTC
Gal10pro-F S. cerevisiae GAL10 promoter, forward primer GGTGGTAATGCCATGTAATATG
Gal4 N-term 3' end of Gal4 DNA binding domain, forward primer GAGTAGTAACAAAGGTCAA
Gal4-AD 3' end of Gal4 activation domain, forward primer AATACCACTACAATGGAT
GFP-F 3' end of GFP, forward primer GGTCCTTCTTGAGTTTGTAAC
IRES-F 3' end of IRES, forward primer TGGCTCTCCTCAAGCGTATT
IRES-R 5' end of IRES, reverse primer CCTCACATTGCCAAAAGACG
LacI-R 5' end of LacI, reverse primer GGCATACTCTGCGACATCGT
LacZ-R 5' end of LacZ, reverse primer GACAGTATCGGCCTCAGGAA
M13 (-21) Forward In lacZ gene TGTAAAACGACGGCCAGT
M13 (-40) In lacZ gene GTTTTCCCAGTCACGAC
M13 Reverse In lacZ gene CAGGAAACAGCTATGAC
pBAD Forward For vectors with E. cotr araBAD promoter, forward primer ATGCCATAGCATTTTTATCC
pBAD Reverse For vectors with E. cotr araBAD promoter, reverse primer GATTTAATCTGTATCAGG
T3 T3 promoter, forward primer GCAATTAACCCTCACTAAAGG
T7 T7 promoter, forward primer TAATACGACTCACTATAGGG
T7 Terminal T7 terminator, reverse primer GCTAGTTATTGCTCAGCGG