 |
 |
v23.34e.1 Update |
 |
|
|
|
|
The new/updated Human data in release 23 are:
Core database
Improved gene set
Addition of ncRNAs to gene set
Addition of selenocysteines to translation model
Addition of ENCODE regions to misc_features
New Affy mappings
Fixed misc_attrib for 32K BACs, changed 'non_ref' to 'name'
EST database
New database
ESTgene database
New database
SNP database
New SNP database from dbSNP 121
Lite database
New database with the new SNP and gene data
Compara database
Recent paralogues added for human
Protein families rebuilt
Orthologues rebuilt
|
|
|
|
|
|
Schema changes in v23 |
|
|
|
|
|
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.
|
|
|
|
|
|
|
New features in v23 |
|
|
|
|
|
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).
|
|
|
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.
|
|
|
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.
|
|
|
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.]
|
|
|
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.
|
|
|
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.
|
|
|
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)
|
|
|
Homo_sapiens 