Annotate-a-genome: Difference between revisions
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imported>Weigang mNo edit summary |
imported>Weigang |
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|| Example | || Example | ||
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| CA382 || B. burgdorferi || Lyme Disease || | | CA382 || B. burgdorferi (California) || Lyme Disease || | ||
* [http://www.ncbi.nlm.nih.gov/nuccore/CP005925.1 main chromosome] | * [http://www.ncbi.nlm.nih.gov/nuccore/CP005925.1 main chromosome] | ||
|| Example | || Example | ||
|- | |- | ||
| CA8 || B. burgdorferi || Lyme Disease || | | CA8 || B. burgdorferi (California) || Lyme Disease || | ||
* [http://www.ncbi.nlm.nih.gov/nuccore/?term=ADMY01000001:ADMY01000007%5Baccn%5D 8 unassembled contigs] | * [http://www.ncbi.nlm.nih.gov/nuccore/?term=ADMY01000001:ADMY01000007%5Baccn%5D 8 unassembled contigs] | ||
|| Example | || Example | ||
|- | |- | ||
| BgVir || B. garinii || Lyme Disease || | | BgVir || B. garinii (Russia) || Lyme Disease || | ||
* [http://www.ncbi.nlm.nih.gov/nuccore/CP003151.1 main chromosome] | * [http://www.ncbi.nlm.nih.gov/nuccore/CP003151.1 main chromosome] | ||
* [http://www.ncbi.nlm.nih.gov/nuccore/CP003201.1 cp26] | * [http://www.ncbi.nlm.nih.gov/nuccore/CP003201.1 cp26] | ||
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|| Example | || Example | ||
|- | |- | ||
| | | NMJW1 || B. garinii (China) || Lyme Disease || | ||
* [http://www.ncbi.nlm.nih.gov/nuccore/CP003866.1 main chromosome] | |||
|| Example | |||
|- | |- | ||
| | | HLJ01 || B. afzelii (China) || Lyme Disease || | ||
* [http://www.ncbi.nlm.nih.gov/nuccore/CP003882.1 main chromosome] | |||
|| Example | |||
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| Example || Example || Example || Example || Example | | Example || Example || Example || Example || Example | ||
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| Example || Example || Example || Example || Example | | Example || Example || Example || Example || Example | ||
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=Protocol= | =Protocol= | ||
# Predict genes with Glimmer if necessary | # Predict genes with Glimmer if necessary | ||
Revision as of 20:38, 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 | |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
| Example | Example | Example | Example | Example |
Protocol
- Predict genes with Glimmer if necessary
- Predict orthologs with reciprocal BLAST
- Load into database
- Visualize results using synteny browser