Difference between revisions of "Mpetredi Week 13"

Revision as of 18:19, 21 November 2013

11/19/2013

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=~
Copied link to Eclipse
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

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.
Name of export file is Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb

@@ Line 26: / Line 26: @@
 #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.
+#Name of export file is Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb
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