Annotate-a-genome

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	main chromosome cp26 plasmid lp54 plasmid	Example
CA382	B. burgdorferi (California)	Lyme Disease	main chromosome	Example
CA8	B. burgdorferi (California)	Lyme Disease	8 unassembled contigs	Example
BgVir	B. garinii (Russia)	Lyme Disease	main chromosome cp26 lp54	Example
NMJW1	B. garinii (China)	Lyme Disease	main chromosome	Example
HLJ01	B. afzelii (China)	Lyme Disease	main chromosome	Example
Ly	B. duttonii (Tanzania)	Relapsing Fever	main chromosome lp23 (homolog of cp26 in LD genomes) Many other plasmids (not to include)	Example
A1	B. recurrentis (Ethiopia)	Relapsing Fever	main chromosome lp124 (homologous to lp54 in LD genomes) lp23	Example
DAH	B. hermsii (Washington State)	Relapsing Fever	main chromosome	Example
91E135	B. turicatae (Texas)	Relapsing Fever	main chromosome	Example
Achema	B. crocidurae (Mauritania)	Relapsing Fever	main chromosome Many unassembled plasmids (not to include)	Example
HR1	B. parkeri (??)	Relapsing Fever	main chromosome	Example
LB-2001	B. miyamotoi (Northeast US)	Relapsing Fever	main chromosome	Example

Protocol

1. Obtain genome accession from the genome links and fetch sequences:

./bioseq -z 'b31_accession' -o 'genbank' > b31.gb # Reference genome for ortholog identification. Choose main, cp26, or lp54
./bioseq -z 'gb_accession' -o 'genbank' > new.gb
./gb2fas -n b31.gb > b31.nuc # Extract CDS
./gb2fas -n new.gb > new.nuc
./bioseq -t b31.nuc > b31.pep # Translate (and remove those with internal stop codons)
./bioseq -t new.nuc > new.pep

1. Predict orthologs with reciprocal BLAST
   1. Prepare BLAST databases
2. Load into database
3. Visualize results using synteny browser