Biology 490 - Research Projects in Molecular Genetics

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LINKS

BIOINFORMATICS

Biology 490 Links

[Mostly external links - see the announcements/handouts page for most internal resources]

About C. elegans from WormClassroom
Introduction to C. elegans from C. elegans II at the NCBI bookshelf

For C. elegans neuronal function (& biopterin genes) projects:

The neuronal genome of C. elegans (Wormbook)
BH4/biopterin-related information

For C. elegans neuronal patterning projects:

Animal Development Lecture & Lab (Bio 376)
Lin-39-related information
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.

Sequence Analysis Links

Databases / Portals

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

The NCBI Handbook

BLAST readings:

The BLAST Sequence Analysis Tool - read through the section 'BLAST Output: 2. The Hit Table'

BLAST page - look under 'Basic BLAST' heading for the standard types of query - blastn, blastp, blastx, tblastn, tblastx
There is plenty of additional information available on this site about BLAST and related programs.

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.
ClustalW2 for multiple sequence alignment
FGENESH - a gene prediction program
NCBI BLAST Server
Reverse Complement Tool 0

Visualization Tools

FirstGlance in Jmol
NCBI - Structure for structure files