Pseudomonas population genomics: Difference between revisions

Revision as of 18:34, 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

Gene	Alignment	Notes
fleN	File:Xxx	Conserved Domain
fleQ	File:Xxx	Conserved Domain
flhf	File:Xxx	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 12: / Line 12: @@
 ## Reconstruct phylogenetic tree
 ## Run PAML tests
+==Update: June 18, 2013==
+{| class="wikitable"
+! Gene !! Alignment !! Tree !! Notes
+|-
+| fleN || [[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]] ||[[File:PGL2vector-map.png|200px]] || [http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?INPUT_TYPE=live&SEQUENCE=AEV61607.1 Conserved Domain]
+|-
+| flhf || [[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]
+|-
+|}
 ==Benchmark: June 11, 2013==