| Primary Annotation Sites | |
|---|---|
| CGAT SEED Viewer for Ammonifex |
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| Manatee for B. megaterium |
RAST SEED Viewer for B. meg |
| Background Information and Literature Research Sites |
|---|
| Wikipedia |
| Todar's Online Textbook of Microbiology |
| Medical Microbiology Textbook from the University of South Carolina. You probably want to go to Bacteriology |
| ***PubMed |
| Useful resources on KEGG |
|---|
| KEGG Home page and table of contents |
| KEGG Organisms List of all organisms in KEGG, along with their 3 letter abbreviations |
| KEGG Pathways List of all pathways and subsystems diagrammed in KEGG |
| Manet A more colorful version of the KEGG maps, coded by phylogeny. |
| NCBI Resources |
|---|
| NCBI Home page |
| ***NCBI Blast You probably want "protein blast", in the Basic Blast section. |
| NCBI PubMed Literature searaches |
| NCBI Taxonomy Browser Paste the taxon ID (the 6 numbers after the "fig|" into the box and get domain and phylum information. |
| CDD Conserved Domains database at NCBI, an alternative to HMMs |
| Other Useful Sites |
|---|
| ***UniProt Good text search for gene names, symbols, organisms, etc. AND, good BLAST search. The database is Swiss-Prot and TrEMBL combined. Swiss-Prot entries are manually curated, while TrEmBL entries aren't. (Note: this is a beta version. The older version is here |
| Metacyc Biochemical pathways, an alternative to KEGG |
| PFAM HMM Search, with links to the families |
| InterPro Scans several different databases. (Also has the coolest "in progress" indicator) |
| Protein Data Bank (PDB) Structural Information about proteins |
| BRENDA Vast amounts of info about individual enzymes |
| Resources at the J. Craig Venter Institute (formerly known as TIGR) |
|---|
| TIGR CMR Comprehensive Microbial Resource. Lots of info |
| TIGR HMM Search tool Very useful, but a bit slow. |
| TIGR Fams List of all TIGR Fams by number, with links to info about each |
| TIGR Genome Properties Which gene functions should be present in various subsytems, according to TIGR |
| Multiple Sequence Alignment |
|---|
| MUSCLE |
| T-COFFEE |
| CLUSTAL-W I don't recommend this one: it is a very primitive algorithm compared to the others. |
| Specialized B. megaterium resources |
|---|
| B meg annotation progress site |
| B meg BLAST search Also, get DNA sequence by gene ID or chromosome position, translate DNA to protein |
| Search B meg annotation , or interconvert TIGR and RAST gene IDs |