Difference between revisions of "Update Matrix WS207"
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|Can you do a blast searches on the appropriate genomes?<br>http://dev.wormbase.org/db/searches/blast_blat | |Can you do a blast searches on the appropriate genomes?<br>http://dev.wormbase.org/db/searches/blast_blat | ||
− | | | + | | see matrix below |
| Create Blast DBs | | Create Blast DBs | ||
|- | |- | ||
|Can you do a blat search on the appropriate genomes?<br>http://dev.wormbase.org/db/searches/blast_blat | |Can you do a blat search on the appropriate genomes?<br>http://dev.wormbase.org/db/searches/blast_blat | ||
− | | | + | | see matrix below |
|Create Blat DBs | |Create Blat DBs | ||
|- | |- | ||
|Does ePCR work? <br> http://dev.wormbase.org/db/searches/epcr | |Does ePCR work? <br> http://dev.wormbase.org/db/searches/epcr | ||
− | | | + | | Search by position from example works |
|Create ePRC DBs | |Create ePRC DBs | ||
|- | |- | ||
|Are the appropriate tracks visible on the appropriate genomes <br>http://dev.wormbase.org/db/seq/sequence?name=AC7;class=Sequence | |Are the appropriate tracks visible on the appropriate genomes <br>http://dev.wormbase.org/db/seq/sequence?name=AC7;class=Sequence | ||
− | | | + | | ok |
| Load GFF DBs | | Load GFF DBs | ||
|- | |- | ||
|Is the EST aligner working? <br>http://dev.wormbase.org/db/seq/aligner | |Is the EST aligner working? <br>http://dev.wormbase.org/db/seq/aligner | ||
− | | | + | | ok |
| Load GFF DBs | | Load GFF DBs | ||
|- | |- | ||
|Is the Gene Details Page working? <br>http://dev.wormbase.org/db/gene/gene?name=amx-2;class=Gene;details=1;dna=B0019.1 | |Is the Gene Details Page working? <br>http://dev.wormbase.org/db/gene/gene?name=amx-2;class=Gene;details=1;dna=B0019.1 | ||
− | | | + | | ok |
| Load GFF DBs | | Load GFF DBs | ||
|- | |- | ||
|Are the supplementary GFF tracks available <br> http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ | |Are the supplementary GFF tracks available <br> http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ | ||
− | | | + | | ok |
| Load GFF DBs | | Load GFF DBs | ||
|- | |- | ||
|Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/ | |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/ | ||
− | | | + | | see matrix below |
| Load GFF DBs | | Load GFF DBs | ||
|- | |- | ||
|Are the Genetic Limit Tracks available <br> http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ | |Are the Genetic Limit Tracks available <br> http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ | ||
− | | | + | | ok |
| Build and Load GFF Patches | | Build and Load GFF Patches | ||
|- | |- | ||
| Are protein motifs available on the Protein page?<br>http://dev.wormbase.org/db/seq/protein?name=T21C12.1;class=Protein | | Are protein motifs available on the Protein page?<br>http://dev.wormbase.org/db/seq/protein?name=T21C12.1;class=Protein | ||
− | | | + | | ok |
| Build and Load GFF Patches | | Build and Load GFF Patches | ||
|- | |- | ||
|Can you do a disease search?<br>http://dev.wormbase.org/db/orthology/disease | |Can you do a disease search?<br>http://dev.wormbase.org/db/orthology/disease | ||
− | | | + | | ok |
| Compile orthology resources | | Compile orthology resources | ||
|- | |- | ||
|Can you list diseases for a gene?<br>http://dev.wormbase.org/db/orthology/disease?related=WBGene00006803 | |Can you list diseases for a gene?<br>http://dev.wormbase.org/db/orthology/disease?related=WBGene00006803 | ||
− | | | + | | ok |
| Compile orthology resources | | Compile orthology resources | ||
|- | |- | ||
|Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | ||
− | | | + | | ok |
| Compile interaction resources | | Compile interaction resources | ||
|- | |- | ||
|Can you list the available position matrices?<br>http://dev.wormbase.org/db/seq/position_matrix?list=all | |Can you list the available position matrices?<br>http://dev.wormbase.org/db/seq/position_matrix?list=all | ||
− | | | + | | ok |
| Compile position matrices | | Compile position matrices | ||
|- | |- | ||
|Can you run a CLUSTAL search? <br> http://dev.wormbase.org/db/seq/show_mult_align | |Can you run a CLUSTAL search? <br> http://dev.wormbase.org/db/seq/show_mult_align | ||
− | | | + | | ok |
| Update CLUSTAL database | | Update CLUSTAL database | ||
|- | |- | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
+ | {| cellpadding="5" border="1" | ||
+ | |||
+ | |- | ||
+ | ! GENOME MATRIX | ||
+ | |- | ||
+ | ! species | ||
+ | ! Blastn<br>http://dev.wormbase.org/db/searches/blast_blat | ||
+ | ! Blastp<br> | ||
+ | ! Blat<br> | ||
+ | ! GBrowse | ||
+ | |- | ||
+ | |<i>C elegans</i> | ||
+ | | ok | ||
+ | | ok | ||
+ | |troubleshooting | ||
+ | | http://dev.wormbase.org/db/seq/gbrowse/c_elegans/<br>ok | ||
+ | |- | ||
+ | |<i>C briggsae</i> | ||
+ | | ok | ||
+ | | ok | ||
+ | | troubleshooting | ||
+ | | http://dev.wormbase.org/db/seq/gbrowse/c_briggsae/?name=chrI%3A80000..120000<br>ok | ||
+ | |- | ||
+ | |<i>C brenneri</i> | ||
+ | | ok | ||
+ | | ok | ||
+ | | N/A | ||
+ | | http://dev.wormbase.org/db/seq/gbrowse/c_brenneri/#search<br>ok | ||
+ | |- | ||
+ | |<i>C remanei</i> | ||
+ | | troubleshooting<br>nixed option in the meantime | ||
+ | | troubleshooting<br>nixed option in the meantime | ||
+ | | troubleshooting<br>nixed option in the meantime | ||
+ | | http://dev.wormbase.org/db/seq/gbrowse/c_remanei/?name=CRE02801<br>ok | ||
+ | |- | ||
+ | |<i>C japonica</i> | ||
+ | | ok | ||
+ | | N/A | ||
+ | | N/A | ||
+ | | http://dev.wormbase.org/db/seq/gbrowse/c_japonica/?name=Cjap_Contig2%3A140000..180000<br>ok | ||
+ | |- | ||
+ | |<i>M hapla</i> | ||
+ | | ok | ||
+ | | N/A | ||
+ | | N/A | ||
+ | | http://dev.wormbase.org/db/seq/gbrowse/m_hapla/?name=MhA1_Contig0<br>ok | ||
+ | |- | ||
+ | |<i>M incognita</i> | ||
+ | | ok | ||
+ | | N/A | ||
+ | | N/A | ||
+ | |http://dev.wormbase.org/db/seq/gbrowse/m_incognita/#search<br>ok | ||
+ | |- | ||
+ | |<i>B malayi</i> | ||
+ | | ok | ||
+ | | N/A | ||
+ | | N/A | ||
+ | | debugging: names of the Gene Models not coming up in browser as well as details page | ||
+ | |- | ||
+ | |<i>P pacificus</i> | ||
+ | | ok | ||
+ | | ok | ||
+ | | N/A | ||
+ | | http://dev.wormbase.org/db/seq/gbrowse/p_pacificus/#search<br>ok | ||
+ | |- | ||
+ | |<i>H contortus</i> | ||
+ | | TBA | ||
+ | | TBA | ||
+ | | N/A | ||
+ | | http://dev.wormbase.org/db/seq/gbrowse/h_contortus/#search<br>ok | ||
+ | |||
+ | |||
+ | |||
+ | [[Category:Developer documentation]] |
Latest revision as of 18:20, 17 August 2010
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 |
see matrix below | Create Blast DBs |
Can you do a blat search on the appropriate genomes? http://dev.wormbase.org/db/searches/blast_blat |
see matrix below | Create Blat DBs |
Does ePCR work? http://dev.wormbase.org/db/searches/epcr |
Search by position from example works | Create ePRC DBs |
Are the appropriate tracks visible on the appropriate genomes http://dev.wormbase.org/db/seq/sequence?name=AC7;class=Sequence |
ok | Load GFF DBs |
Is the EST aligner working? http://dev.wormbase.org/db/seq/aligner |
ok | 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 |
ok | Load GFF DBs |
Are the supplementary GFF tracks available http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ |
ok | Load GFF DBs |
Are the GBrowsers for the various species working http://dev.wormbase.org/db/seq/gbrowse/ |
see matrix below | Load GFF DBs |
Are the Genetic Limit Tracks available http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ |
ok | 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 |
ok | Build and Load GFF Patches |
Can you do a disease search? http://dev.wormbase.org/db/orthology/disease |
ok | Compile orthology resources |
Can you list diseases for a gene? http://dev.wormbase.org/db/orthology/disease?related=WBGene00006803 |
ok | Compile orthology resources |
Can you list interactions? http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 |
ok | Compile interaction resources |
Can you list the available position matrices? http://dev.wormbase.org/db/seq/position_matrix?list=all |
ok | Compile position matrices |
Can you run a CLUSTAL search? http://dev.wormbase.org/db/seq/show_mult_align |
ok | Update CLUSTAL database |