started adding functional genomics entries

misc-scripts/analysis_description/analysis.descriptions

@@ -352,3 +352,41 @@
 351	zfish_protein	Zebrafish proteins from <a rel="external" href="http://uniprot.org">UniProtKB</a> are aligned to the genome using <a rel="external" href="http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;volume=14&amp;firstpage=988&amp;resourcetype=HWCIT">GeneWise</a>.	Zebrafish prot.	1
 352	brepepP	Caenorhabditis brenneri proteins aligned by WU-BlastP	BrepepP	1
 353	brepepX	Caenorhabditis brenneri proteins aligned by WU-BlastX	BrepepX	1
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+#add new entries for core databases above, the following are for functional genomics
+500	Nessie	Hidden Markov Model based predictions based on tiling array data	Nessie (TilingHMM)	1
+501	HitList	Custom hit list	HitList	1
+502	SupervisedHMM	Supervised Hidden Markov Model	SupervisedHMM	1
+503	PHALANX_ProbeAlign	Genomic alignments for PHALANX arrays	PHALANX_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
+504	ILLUMINA_WG_ProbeTranscriptAlign	Transcript alignments for ILLUMINA_WG arrays	ILLUMINA_WG_ProbeTranscriptAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
+505	cisRED	cisRED motif search (www.cisred.org)	cisRED	1	{'type' => 'regulatory_regions', 'name' => 'cisRED Motifs', 'colourset' => 'synteny', 'display' =>'off' }
+506	Parzen	Solexa clusters	Parzen	1
+507	RegulatoryRegion	Union of focus features, features overlapping focus features, and features that are contained within those	RegulatoryRegion	1	{'type' => 'fg_regulatory_features', 'name' => 'Reg. Feats',  'display' =>'off', 'depth' => 10, 'default' => {'contigviewbottom' => 'normal', 'generegview' => 'normal'} }
+508	CODELINK_ProbeAlign	Genomic alignments for CODELINK arrays	CODELINK_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
+509	AFFY_ST_ProbeTranscriptAlign	Transcript alignments for AFFY_ST arrays	AFFY_ST_ProbeTranscriptAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
+510	Wiggle	Solexa clusters from wiggle data	Parzen	1
+511	AGILENT_ProbeTranscriptAlign	Transcript alignments for AGILENT arrays	AGILENT_ProbeTranscriptAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
+512	LiftOver	Remapping to new assembly performed by LiftOver	LiftOver	1
+513	NestedMICA	BioTIFFIN	BioTIFFIN	1	{ 'type' => 'regulatory_regions', 'key' => 'feature_set', 'name' => 'REDfly/BioTIFFIN', 'colourset' => 'synteny', 'display' =>'off' }
+514	SangerPCR	Ratio generated by standard Sanger PCR array processing	SangerPCR	1
+515	VSN_GLOG	Generalised log transformation based on VSN variance stabilised scores	VSN_GLOG	1	{'type' => 'histone_modifications', 'name' => 'Histone Modifications', 'display' => 'off', 'renderers' => {'off' => 'Off',  'tiling' => 'Normal'} }
+516	Nessie_NG_STD_2	Hidden Markov Model based predictions based on tiling array data	HMM predictions based on tiling array data	1	{'type' => 'ctcf', 'name' => 'CTCF', 'display' => 'off', 'renderers' => {'off' => 'Off',  'tiling' => 'Normal'} }
+517	AFFY_ST_ProbeAlign	Genomic alignments for AFFY_ST arrays	AFFY_ST_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
+518	VendorMap	Original mapping provided by Array Vendor	Vendor mapping	1
+519	AFFY_UTR_ProbeTranscriptAlign	Transcript alignments for AFFY_UTR arrays	AFFY_UTR_ProbeTranscriptAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
+520	AFFY_UTR_ProbeAlign	Genomic alignments for AFFY_UTR arrays	AFFY_UTR_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
+521	RawValue	Raw value	Raw value	1
+522	VISTA	VISTA Enhancer Assay (http://enhancer.lbl.gov/)	VISTA	1
+523	REDfly CRM	REDfly CRMs	REDfly CRM	1	{ 'type' => 'regulatory_regions', 'key' => 'feature_set', 'name' => 'REDfly/BioTIFFIN', 'colourset' => 'synteny', 'display' =>'off' }
+524	miRanda	miRanda microRNA target prediction (http://microrna.sanger.ac.uk/targets)	miRanda	1	{'type' => 'regulatory_regions', 'key' => 'feature_set', 'name' => 'cisRED/miRanda/VISTA', 'colourset' => 'synteny', 'display' =>'off' }
+525	REDfly TFBS	REDfly TFBSs	REDfly TFBSs	1	{ 'type' => 'regulatory_regions', 'key' => 'feature_set', 'name' => 'REDfly/BioTIFFIN', 'colourset' => 'synteny', 'display' =>'off' }
+526	Co-occurrence Overlap	Co-occurrence of overlapping feature types	Co-occurrence Overlap	1
+527	PHALANX_ProbeTranscriptAlign	Transcript alignments for PHALANX arrays	PHALANX_ProbeTranscriptAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
+528	AGILENT_ProbeAlign	Genomic alignments for AGILENT arrays	AGILENT_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
+529	ILLUMINA_WG_ProbeAlign	Genomic alignments for ILLUMINA_WG arrays	ILLUMINA_WG_ProbeAlign	1	{'type' => '_oligo', 'key' => 'array_chip', 'colourset' => 'feature', 'display' =>'off' }
+530	T.Biweight	Weighted mean standardisation using the one step Tukey Biweight algorithm	Tukey Biweight	1
+531	WindowInterval	Window Interval	WindowInterval	1	
+532	probe2transcript	Microarray probes from manufacturers are aligned to the genome by Ensembl, if the probe sequences are provided. The mapping is a two-step procedure outlined <a href="/info/docs/microarray_probe_set_mapping.html">here</a>.	Probe2Transcript Annotation	0