Difference between revisions of "Mpetredi Week 13"

Revision as of 18:21, 21 November 2013

Mitchell Petredis

[[Team Name]]

11/19/2013

Lab Progression

1. Attempting to find URL pattern of S. meliloti
   1. Navigated to model organism database (link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01)
   2. Clicked on all 3 GenBank Accession.Versions and looked for locus ID formatting
      • [Complete Chromosome]
        • SMc#####
      • [plasmid pSymB]
        • SMb#####
          • NOTE: in the XML file (from [[Team Name]]) appears as SM_b for gene ID; uses SMb for ORF name
      • [plasmid pSymA]
        • SMa####
   3. Copy any locus ID that follows the format of the options above
   4. After many trials, the general link looks like this: http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=~
2. Copied link to Eclipse
3. Opened the .gdb file (from [[Team Name]]) in Microsoft Access to determine how GeneIDs look like
   1. Open OrderedLocusNames and look at how IDs are named (R.####, where "." is either a letter or a number) and how many records are displayed
      • 4712 records

11/21/2013

Lab Progression

1. Started a new export based on latest, custom build of gmbuilder (GenMAPP Builder 2.0b72).
   • Except for gmbuilder, I used all files posted on [[Team Name]] under "Important Files" section.
2. Name of export file is Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb