Difference between revisions of "Update Matrix WS220"

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Revision as of 22:39, 11 November 2010

GENOME MATRIX
species Blastn
http://dev.wormbase.org/db/searches/blast_blat
Blastp
Blat
GBrowse
C elegans ok ok troubleshooting http://dev.wormbase.org/db/gb2/gbrowse/c_elegans/
ok
C briggsae ok ok troubleshooting http://dev.wormbase.org/db/gb2/gbrowse/c_briggsae/?name=chrI%3A80000..120000
page didn't render
C brenneri ok ok N/A http://dev.wormbase.org/db/gb2/gbrowse/c_brenneri/#search
ok
C remanei ok ok N/A http://dev.wormbase.org/db/gb2/gbrowse/c_remanei/?name=CRE02801
ok
C japonica ok N/A N/A http://dev.wormbase.org/db/gb2/gbrowse/c_japonica/?name=Cjap_Contig2%3A140000..180000
ok
M hapla ok N/A N/A http://dev.wormbase.org/db/gb2/gbrowse/m_hapla/?name=MhA1_Contig0
ok
M incognita ok N/A N/A http://dev.wormbase.org/db/gb2/gbrowse/m_incognita/#search
ok
B malayi ok N/A N/A http://dev.wormbase.org/db/gb2/gbrowse/b_malayi/?name=Bmal_supercontig12883
ok
P pacificus ok ok N/A http://dev.wormbase.org/db/gb2/gbrowse/p_pacificus/#search
ok
Check Note Related Compile Step
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
ok Compile Ontology Resources
Are the Ontology related summary pages working? ok 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
ok 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/gb2/gbrowse/c_elegans/
ok Load GFF DBs
Are the GBrowsers for the various species working
http://dev.wormbase.org/db/gb2/gbrowse/
see matrix below Load GFF DBs
Are the Genetic Limit Tracks available
http://dev.wormbase.org/db/gb2/gbrowse/c_elegans/
ok Build and Load GFF Patches
Are protein motifs available on the Protein page?
http://dev.wormbase.org/db/gb2/gbrowse/c_elegans/
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
Is strain data available? ok run Strain update
Are all the files for FTP present? ok