Useful links for those doing C. elegans RNAi projects:

• Introduction to C. elegans from C. elegans II at the NCBI bookshelf

• Animal Development Lecture & Lab (Bio 376)
• The Wnt Homepage by Roel Nusse
• Wormbook - see especially the sections on signal transduction, including
  • Wnt signaling
  • RTK/Ras/MAPK signaling, and
  • Roles of chromatin factors in C. elegans development
    Note that chromatin structure regulators in the Polycomb and trithorax classes (SET domain proteins) are known regulators of Hox genes, like lin-39.

BLAST readings:

Sequence Analysis Links

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

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.
• VecScreen - to spot likely vector sequence in your clone
• Vector images, vector cloning site sequences and other information
• ClustalW2 for multiple sequence alignment
• FGENESH - a gene prediction program
• NCBI BLAST Server
• Reverse Complement Tool
• Site with links to sequence chromatogram readers; for Mac OSX, I prefer 4Peaks.
• Interpreting a Phred Q20 score, from a sequencing center FAQ

Primer design info and tools

• NEBuilder - NEB Gibson Assembly planner
• 382 sequence analysis folder
• Primer3
• Reverse e-PCR
• NCBI Primer-BLAST
• List of Research Genetics C. elegans primers

Visualization Tools

• FirstGlance in Jmol