Difference between revisions of "Update Matrix WS206"
From WormBaseWiki
Jump to navigationJump to searchLine 111: | Line 111: | ||
! Blat | ! Blat | ||
! ePCR | ! ePCR | ||
+ | ! GBrowse | ||
|- | |- | ||
|<i>C elegans</i> | |<i>C elegans</i> | ||
| <br> | | <br> | ||
+ | | <br> | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
Line 119: | Line 121: | ||
|<i>C briggsae</i> | |<i>C briggsae</i> | ||
| <br> | | <br> | ||
+ | | <br> | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
Line 124: | Line 127: | ||
|<i>C brenneri</i> | |<i>C brenneri</i> | ||
| <br> | | <br> | ||
+ | | <br> | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
Line 129: | Line 133: | ||
|<i>C bruggia</i> | |<i>C bruggia</i> | ||
| <br> | | <br> | ||
+ | | <br> | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
Line 134: | Line 139: | ||
|<i>C japonica</i> | |<i>C japonica</i> | ||
| <br> | | <br> | ||
+ | | <br> | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
Line 139: | Line 145: | ||
|<i>M hapla</i> | |<i>M hapla</i> | ||
| <br> | | <br> | ||
+ | | <br> | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
Line 144: | Line 151: | ||
|<i>M incognita</i> | |<i>M incognita</i> | ||
| <br> | | <br> | ||
+ | | <br> | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
Line 149: | Line 157: | ||
|<i>B malayi</i> | |<i>B malayi</i> | ||
| <br> | | <br> | ||
+ | | <br> | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
Line 154: | Line 163: | ||
|<i>P pacificus</i> | |<i>P pacificus</i> | ||
| <br> | | <br> | ||
+ | | <br> | ||
| <br> | | <br> | ||
| <br> | | <br> |
Revision as of 16:23, 17 September 2009
Check | Note | Related Compile Step |
---|---|---|
Have directories been created for given release in /u/l/w/databases? | Create Data Directories | |
Has a wormbase_RELEASE directory been created in /u/l/w/acedb? | Mirror and Unpack AceDB files | |
Is the Dev site running with the correct release number? | Mirror and Unpack AceDB files | |
Is the wormbase pointer linked to the newly created acedb? | Mirror and Unpack AceDB files | |
Is the database running and providing the correct version number? | Mirror and Unpack AceDB files | |
Are the correct ontology files in /u/l/w/databases? | Mirror Ontology from Sanger | |
Were the additional ontology files generated? | Compile Ontology Resources | |
Is the Multi-Ontology Search Running? URL: http://dev.wormbase.org/db/ontology/search |
Compile Ontology Resources | |
Are the Ontology related summary pages working? | Compile Ontology Resources | |
Can you do a blast searches on the appropriate genomes? http://dev.wormbase.org/db/searches/blast_blat |
Create Blast DBs | |
Can you do a blat search on the appropriate genomes? http://dev.wormbase.org/db/searches/blast_blat |
Create Blat DBs | |
Does ePCR work? http://dev.wormbase.org/db/searches/epcr |
Create ePRC DBs | |
Are the appropriate tracks visible on the appropriate genomes http://dev.wormbase.org/db/seq/sequence?name=AC7;class=Sequence |
Load GFF DBs | |
Is the EST aligner working? http://dev.wormbase.org/db/seq/aligner |
Load GFF DBs | |
Is the Gene Details Page working? http://dev.wormbase.org/db/gene/gene?name=amx-2;class=Gene;details=1;dna=B0019.1 |
Load GFF DBs | |
Are the supplementary GFF tracks available http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ |
Load GFF DBs | |
Are the GBrowsers for the various species working http://dev.wormbase.org/db/seq/gbrowse/ |
Load GFF DBs | |
Are the Genetic Limit Tracks available http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ |
Build and Load GFF Patches | |
Are protein motifs available on the Protein page? http://dev.wormbase.org/db/seq/protein?name=T21C12.1;class=Protein |
Build and Load GFF Patches | |
Can you do a disease search? http://dev.wormbase.org/db/orthology/disease |
Compile orthology resources | |
Can you list diseases for a gene? http://dev.wormbase.org/db/orthology/disease?related=WBGene00006803 |
Compile orthology resources | |
Can you list interactions? http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 |
Compile interaction resources | |
Can you list the available position matrices? http://dev.wormbase.org/db/seq/position_matrix?list=all |
Compile position matrices | |
Can you run a CLUSTAL search? http://dev.wormbase.org/db/seq/show_mult_align |
Update CLUSTAL database |
species | Blast | Blat | ePCR | GBrowse |
---|---|---|---|---|
C elegans | ||||
C briggsae | ||||
C brenneri | ||||
C bruggia | ||||
C japonica | ||||
M hapla | ||||
M incognita | ||||
B malayi | ||||
P pacificus |