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v23.1a.1 Update |
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The new/updated Chicken data in release 23 are:
Core database
BAC end dataset added
SNP database
New SNP database from BGI data
Lite database
New database with the new SNP data
Compara database
Protein families rebuilt
Orthologues rebuilt
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Schema changes in v23 |
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SNP database
In table "Freq", changed "count" column from smallint(5) unsigned changed to float
In table "SubSNP", added a column "strand_to_rs" tinyint(4)
Compara database
In table "method_link_species", changed index from UNIQUE method_link_id
(method_link_id,species_set,genome_db_id) to KEY method_link_id
(method_link_id,species_set,genome_db_id) to allow intra-species data set
such as the new human paralogues set.
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New features in v23 |
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MultiContigView
Can now locate homologous regions by gene homology, as well as the original
DNA-DNA alignment method. Orthologues on GeneView are now linked into
MultiContigView.
Can show links between homologous transcripts (select "Join transcripts" from the "Compara" menu).
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GeneView
Now has a link ("Sequence Markup") that displays the genomic sequence of
the gene, optionally marked-up with exons, SNPs, and line numbers.[e.g.]
The gene neighbourhood image at the top of GeneView now has a Features
drop-down menu, similar to the menus on ContigView. This menu provides
options for displaying SNPs and different transcripts on the image.
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BLASTView
Addition of an ncRNA BLAST database for human
The SETUP page has been extended:
- Query sequences can be loaded via ID (EMBL/Uniprot/RefSeq) e.g. NM_002931
Searches can be run using one of five pre-set sensitivity levels; exact,
near-exact, near-exact (oligo), local mismatch, and distant homology.
New features on the DISPLAY page:
- The top 'n' alignments (various sort options) to display can now be
specified.
- There is a new graph that displays the location of matches on the length
of the query sequence.
- For the alignment summary table, there are new options to allow the
alignment location to de displayed in any coordinate system.
- A new page (follow the "[G]" link) shows genomic sequence (with
user-definable coordinate system, orientation, and length of flanking
sequence) with the Exons and SNPs highlighted.
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AlignView
This page has been extended to display Compara DNA-DNA and gene homology
alignments, in a variety of different formats. These alignments can be
reached via GeneView (for homologues) or from the Compara tracks in
ContigView. [e.g.]
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GeneSNPView
The table at the bottom of the page now displays the SNP type, AA
change, and AA position for all transcripts of the gene.
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FASTAView
Can display data from the core database for mapped Affy identifiers,
including description, locations. and other members of a composite group.
These data are linked to from the mapped Affys on ContigView and GeneView.
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ContigView
New ncRNA tracks ("Features" menu)
New ENCODE region track ("Features" menu)
New tracks for Affy hg_u95b, c, d, and e probesets ("Features" menu)
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Gallus_gallus 