Annotate-a-genome: Difference between revisions
Jump to navigation
Jump to search
imported>Weigang |
imported>Weigang |
||
| Line 60: | Line 60: | ||
|| Example | || Example | ||
|- | |- | ||
| HR1 || B. parkeri || Relapsing Fever | | HR1 || B. parkeri (??) || Relapsing Fever || | ||
* [http://www.ncbi.nlm.nih.gov/nuccore/CP007022.1 main chromosome] | * [http://www.ncbi.nlm.nih.gov/nuccore/CP007022.1 main chromosome] | ||
|| Example | || Example | ||
Revision as of 21:09, 13 February 2014
Project Goals
- Annotate and add newly sequenced Borrelia genomes to BorreliaBase
- Build an informatics pipeline for gene prediction, ortholog calls, databasing, and synteny analysis
Download genome sequences from GenBank
| Strain | Species | Group | Genome Sequences | Notes |
|---|---|---|---|---|
| B31 | B. burgdorferi (reference genome) | Lyme Disease | Example | |
| CA382 | B. burgdorferi (California) | Lyme Disease | Example | |
| CA8 | B. burgdorferi (California) | Lyme Disease | Example | |
| BgVir | B. garinii (Russia) | Lyme Disease | Example | |
| NMJW1 | B. garinii (China) | Lyme Disease | Example | |
| HLJ01 | B. afzelii (China) | Lyme Disease | Example | |
| Ly | B. duttonii (Tanzania) | Relapsing Fever |
|
Example |
| A1 | B. recurrentis (Ethiopia) | Relapsing Fever | Example | |
| DAH | B. hermsii (Washington State) | Relapsing Fever | Example | |
| 91E135 | B. turicatae (Texas) | Relapsing Fever | Example | |
| Achema | B. crocidurae (Mauritania) | Relapsing Fever |
|
Example |
| HR1 | B. parkeri (??) | Relapsing Fever | Example | |
| LB-2001 | B. miyamotoi (Northeast US) | Relapsing Fever | Example |
Protocol
- Predict genes with Glimmer if necessary
- Predict orthologs with reciprocal BLAST
- Load into database
- Visualize results using synteny browser