Pseudomonas population genomics: Difference between revisions
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# Material and Methods | # Material and Methods | ||
## Protein ortholog data: [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=105676&start=1583956&stop=1584798&replicon_id_reference=136&alphabet=protein&limit_to_species=false fleN], [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=104960&start=1187587&stop=1189059&replicon_id_reference=136&alphabet=protein&limit_to_species=false fleQ], [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=105674&start=1582528&stop=1583817&replicon_id_reference=136&alphabet=protein&limit_to_species=false flhF] | ## Protein ortholog data: [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=105676&start=1583956&stop=1584798&replicon_id_reference=136&alphabet=protein&limit_to_species=false fleN], [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=104960&start=1187587&stop=1189059&replicon_id_reference=136&alphabet=protein&limit_to_species=false fleQ], [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=105674&start=1582528&stop=1583817&replicon_id_reference=136&alphabet=protein&limit_to_species=false flhF] | ||
## Protocol: | ## Protocol: | ||
### Fasta headers are too long for tree, run: [[File:renamer.pl renamer]] editing/rule (script name?); Alignment (tool and command); Phylogeny; Tree display (R commands) | |||
{| class="wikitable" | {| class="wikitable" | ||
! Gene !! Alignment !! Tree !! Notes | ! Gene !! Alignment !! Tree !! Notes |
Revision as of 20:47, 18 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 1-8
(I will write a bash script that does this and runs the program) https://www.dropbox.com/s/lpxxbkxeyw7frrn/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
Update: June 18, 2013
- Material and Methods
- Protein ortholog data: fleN, fleQ, flhF
- Protocol:
- Fasta headers are too long for tree, run: File:Renamer.pl renamer editing/rule (script name?); Alignment (tool and command); Phylogeny; Tree display (R commands)
Gene | Alignment | Tree | Notes |
---|---|---|---|
fleN | fleN pep alignment | Conserved Domain | |
fleQ | fleQ pep alignment | Conserved Domain | |
flhf | flhF pep alignment | Conserved Domain |
Benchmark: June 11, 2013
- Finish parsing the genome files to upload the "orf" table (Raymond & Rayees)
- Rayees Parsed genome files: https://www.dropbox.com/sh/k0zktvvmv39op9i/1zBercEky8
- Parsing the ortholog file to upload the "orth_orf" table (Raymond)
- Identify and download fleN, fleQ, and flhF orthologs & align them (Rayees)