Difference between revisions of "Ksherbina Week 9"
From LMU BioDB 2013
(→Lab Notebook: Added sql query) |
(→Lab Notebook: Added instructions to download XML file for V. cholerae) |
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*Download GenMAPP Builder 2.0b70 from http://sourceforge.net/projects/xmlpipedb/files/GenMAPP%20Builder/ | *Download GenMAPP Builder 2.0b70 from http://sourceforge.net/projects/xmlpipedb/files/GenMAPP%20Builder/ | ||
| − | *Download XMLPipeDB | + | *Download XMLPipeDB Match from http://sourceforge.net/projects/xmlpipedb/files/XMLPipeDB%20Match/ |
| + | *Download the UniProt XML file for ''Vibrio cholerae'' | ||
| + | :*Go to the page http://www.uniprot.org/uniprot/?query=organism:243277+keyword:1185 | ||
| + | :*Click the orange [http://www.uniprot.org/uniprot/?query=organism%3a243277+keyword%3a1185&format=* Download] link in the upper right-hand corner of the page. | ||
| + | :*Download the XML file format. | ||
*Use XMLPipeDB Match to count the number of unique gene ideas in the V. cholerae Uniprot XML file. | *Use XMLPipeDB Match to count the number of unique gene ideas in the V. cholerae Uniprot XML file. | ||
Revision as of 02:29, 25 October 2013
| Assignment Description | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 13 | Week 15 |
| Class Journal | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | |||||
| Individual Journal | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 |
| Other | Week 5: Database Wiki |
| Final Project | Team H(oo)KD Project Page | Journal Club Presentation | Project Individual Journal |
Export Information
Version of GenMAPP Builder: 2.0b70
Computer on which export was run: Personal computer
Postgres Database name: VC_KS_20131022_gmb2b70
UniProt XML filename: UniProt_V_cholerae_KSTV_20131022.xml
- UniProt XML version (The version information can be found at the UniProt News Page): UniProt release 2013_10
- Time taken to import: 4.20 minutes
GO OBO-XML filename: go_daily-termdb_KS_20131022.obo-xml
- GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the GO Download page has been unzipped):
- Time taken to import: 8.81 minutes
- Time taken to process: 7.33 minutes
GOA filename: 46.V_cholerae_ATCC_39315_KS_20131022.goa
- GOA version (News on this page records past releases; current information can be found in the Last modified field on the FTP site):
- Time taken to import: 0.10 minutes
Name of .gdb file: Vc-Std_KS_20131022.gdb
- Time taken to export .gdb:
- Start Time: 6:50 pm
- End Time: 9:22 pm
- Link to file: Vc-Std KS 20131022.gdb
Note:
Lab Notebook
- Download GenMAPP Builder 2.0b70 from http://sourceforge.net/projects/xmlpipedb/files/GenMAPP%20Builder/
- Download XMLPipeDB Match from http://sourceforge.net/projects/xmlpipedb/files/XMLPipeDB%20Match/
- Download the UniProt XML file for Vibrio cholerae
- Go to the page http://www.uniprot.org/uniprot/?query=organism:243277+keyword:1185
- Click the orange Download link in the upper right-hand corner of the page.
- Download the XML file format.
- Use XMLPipeDB Match to count the number of unique gene ideas in the V. cholerae Uniprot XML file.
java -jar xmlpipedb-match-1.1.1.jar "VC_[0-9][0-9][0-9][0-9]" < UniProt_V_cholerae_KSTV_20131022
2738 unique matches were found.
java -jar xmlpipedb-match-1.1.1.jar "VC_(A|)[0-9][0-9][0-9][0-9]" < UniProt_V_cholerae_KSTV_20131022
3831 unique matches were found.
- Count the number of unique gene IDs using an SQL query:
select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_(A|)[0-9][0-9][0-9][0-9]'
Count = 3831
