Cloning projects sequencing

• Get a chromatogram reader:
  • For Mac OSX, I prefer 4Peaks; for Windows, try Chromas 2.6.6, still free, or Sequence Scanner, but a form is required.
  • Or ApE (A plasmid Editor) by Wayne Davis - Another excellent choice (with a lot more features than just reading chromatograms) - a free & open source program with both Mac and Windows versions.
  • Or SnapGene (download free version) - another plasmid mapping program (full-featured, both free and paid versions) that has a chromatogram viewer.
• Interpreting a Phred Q20 score, from a sequencing center FAQ
• VecScreen - to spot likely vector sequence in your clone
• View of cloning site region of pCR8/GW/TOPO vector
• Vector images, vector cloning site sequences and other information
  
• NCBI BLAST - Links to all BLAST versions to test your insert sequence after trimming

Databases / Portals

• NCBI Global Cross-database Search
• NCBI - Structure
• EMBL Nucleotide Sequence Database
• DNA Data Bank of Japan
• Kyoto Encyclopedia of Genes and Genomes (KEGG)
• WormBase - C. elegans whole organismal database

Primer design info and tools

• Primer3web - for primer design (shows all options) / Primer3Plus (options hidden under separate tabs)
• NCBI Primer-BLAST - for 'electronic PCR'
• NCBI BLAST - choose Nucleotide BLAST from amplicon testing

Various Analysis Tools

• ExPASy DNA to Protein translation tool
• SIM - Alignment Tool for 2 protein sequences
• Local Alignment Tool for 2 nucleotide sequences - note you must know the relative orientations of the two sequences. If your first pairwise alignment doesn't work, try one sequence in the reverse orientation.
• Reverse Complement Tool
• Clustal_Omega for multiple sequence alignment
• FGENESH - a gene prediction program
• NCBI - BLAST
• NEBuilder - NEB Gibson Assembly planner

Visualization Tools

• iCn3D - NCBI WebGL-based Structure Viewer, including ability to view primary sequence alongside structures
• FirstGlance in Jmol