Pseudomonas population genomics: Difference between revisions
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### "orf": genome_id, locus_tag, start, stop, strand, genome_name, product_name | ### "orf": genome_id, locus_tag, start, stop, strand, genome_name, product_name | ||
### "orth_orf": orth_orf_id, locus_name, genome_id, orth_class | ### "orth_orf": orth_orf_id, locus_name, genome_id, orth_class | ||
## Parsing scripts | ## Parsing scripts | ||
###Rayees Parsing code, requires that you remove columns 9-27 using bash command: <code>cut -c 1-8</code> https://www.dropbox.com/s/dfwsu85bcwzayq7/parser.pl | |||
## Database loading scripts | ## Database loading scripts | ||
#Molecular Evolution of flagellum genes | #Molecular Evolution of flagellum genes | ||
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## Reconstruct phylogenetic tree | ## Reconstruct phylogenetic tree | ||
## Run PAML tests | ## Run PAML tests | ||
==Benchmark: June 11, 2013== | ==Benchmark: June 11, 2013== | ||
# Finish parsing the genome files to upload the "orf" table (Raymond & Rayees) | # Finish parsing the genome files to upload the "orf" table (Raymond & Rayees) | ||
# Parsing the [http://pseudomonas.com/downloadOrthologs.do?strain_id=107 ortholog file] to upload the "orth_orf" table (Raymond) | # Parsing the [http://pseudomonas.com/downloadOrthologs.do?strain_id=107 ortholog file] to upload the "orth_orf" table (Raymond) | ||
# Identify and download fleN, fleQ, and flhF orthologs & align them (Rayees) | # Identify and download fleN, fleQ, and flhF orthologs & align them (Rayees) | ||
Revision as of 17:13, 11 June 2013
Projects
- Build a local genome database
- Database schema:
- "genome": genome_id, strain_name, ncbi_taxid
- "orf": genome_id, locus_tag, start, stop, strand, genome_name, product_name
- "orth_orf": orth_orf_id, locus_name, genome_id, orth_class
- Parsing scripts
- Rayees Parsing code, requires that you remove columns 9-27 using bash command:
cut -c 1-8https://www.dropbox.com/s/dfwsu85bcwzayq7/parser.pl
- Rayees Parsing code, requires that you remove columns 9-27 using bash command:
- Database loading scripts
- Database schema:
- Molecular Evolution of flagellum genes
- Download orthologs
- Reconstruct phylogenetic tree
- Run PAML tests
Benchmark: June 11, 2013
- Finish parsing the genome files to upload the "orf" table (Raymond & Rayees)
- Parsing the ortholog file to upload the "orth_orf" table (Raymond)
- Identify and download fleN, fleQ, and flhF orthologs & align them (Rayees)