Pseudomonas population genomics: Difference between revisions

Revision as of 20:32, 18 June 2013

Build a local genome database
1. Database schema:
  1. "genome": genome_id, strain_name, ncbi_taxid
  2. "orf": genome_id, locus_tag, start, stop, strand, genome_name, product_name
  3. "orth_orf": orth_orf_id, locus_name, genome_id, orth_class
2. Parsing scripts
  1. 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
3. Database loading scripts
Molecular Evolution of flagellum genes
1. Download orthologs
2. Reconstruct phylogenetic tree
3. Run PAML tests

Material and Methods
1. Web links & how did you download the sequences?
2. Protocol: Sequence name editing/rule (script name?); Alignment (tool and command); Phylogeny; Tree display (R commands)

Gene	Alignment	Tree	Notes
fleN	fleN pep alignment	200px	Conserved Domain
fleQ	File:Xxx	200px	Conserved Domain
flhf	flhf pep alignment		Conserved Domain

Finish parsing the genome files to upload the "orf" table (Raymond & Rayees)
1. 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)

@@ Line 20: / Line 20: @@
 ! Gene !! Alignment !! Tree !! Notes
 |-
-| fleN || [[fleN pep alignment]] ||[[File:PGL2vector-map.png|200px]]|| [http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?INPUT_TYPE=live&SEQUENCE=AEV61607.1 Conserved Domain]
+| fleN || [[fleN pep alignment]] ||[[200px]]|| [http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?INPUT_TYPE=live&SEQUENCE=AEV61607.1 Conserved Domain]
 |-
-| fleQ || [[File:xxx]] ||[[File:PGL2vector-map.png|200px]] || [http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?INPUT_TYPE=live&SEQUENCE=AEV61607.1 Conserved Domain]
+| fleQ || [[File:xxx]] ||[[200px]] || [http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?INPUT_TYPE=live&SEQUENCE=AEV61607.1 Conserved Domain]
 |-
-| flhf ||[[flhf pep alignment]]||[[File:PGL2vector-map.png|200px]] || [http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?INPUT_TYPE=live&SEQUENCE=AEV61607.1 Conserved Domain]
+| flhf ||[[flhf pep alignment]]||[[File:flhf.png|200px]] || [http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?INPUT_TYPE=live&SEQUENCE=AEV61607.1 Conserved Domain]
 |-
 |}