GALA: Genome Alignment and Annotation database on Mouse Oct 2003 Freeze
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Query form
Note: Queries are limited to returning 50 million results or less
Only the most common fields are displayed by default, more fields can be accessed by selecting Show on the radio buttons and clicking the Refresh form button. To see an outline of all the fields available click
here
Selections within a list are joined with a
UNION
.
Selections from different lists are joined with an
INTERSECTION
.
Click here to trim the regions and return only the intersecting areas.
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match exact case only
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Genes and Gene Predictions
all genes (default set, Locus Link Genes and Refseq Genes)
Other fields for genes
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EST and mRNA
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Comparative Genomics
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Multiple Alignments
The alignments were generated using
multiz.
Download the alignment files from
UCSC Genome Browser
This data is not available.
Pairwise Alignments
The source of the alignment data is the
UCSC Genome Browser
and
Penn State - Bioinformatics Group
Query
all alignments
Species: mouse vs
human
rat
For help with the pairwise alignment fields below see the
FAQ
.
Minimum length
bp
Minimum identity
%
To use the following 2 fields you must enter both and the 2 fields to the left.
Maximum gap size
bp
Maximum identity step
%
Blat alignments
The source of this data is
UCSC Genome Browser
This data is not available
3-way conserved
The source is
Penn State - Bioinformatics Group
This data is not available.
Net alignments
The source of this data is
UCSC Genome Browser
This data is not available
Regulatory potential
The source is
Penn State - Bioinformatics Group
the scores are displayed as a wiggle track at
UCSC Genome Browser
.
This data is not available.
Regulatory potential scores based on multiple alignments
This data is not available.
PhyloHMM Cons
The source of the PhyloHMM Cons is
UCSC Genome Browser
This data is not available.
Variation and Repeats
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Expression and Regulation
Transcription factor binding sites
The transcription factor binding sites were produced with
tffind
, tfloc, and
TRANSFAC
(free registration required)
Query
all TF binding sites (interval is required)
Conserved binding sites are not available.
To select/add factor names
To select/add factor IDs
Strand
+
-
Score (range between 0.75 and 1)
to
ChIP-chip data from affymetrix
The source is
Human Transcriptome Project
This data is not available
Other fields for expression and regulation
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Mapping and Sequencing
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Restrict search to interval
Enter interval in the format chr7:1000-2000
Note: Items within a proximity of a querys results can be searched using the history page.
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Output
Format of output
FAQ about formats
Index pages
region summary
gene summary
Graphical displays
UCSC Genome Browser user track
Ensembl Genome Browser user track
Laj alignment viewer
text alignment
Mulan
rVista
zPicture
bar graphs
Computer readable formats
text list
BED format
Ensembl upload file
Lav-formatted file
Single table queries only
Tab delimited table columns
Submit buttons (for help
click here
) (for limitations
click here
)
but don't run the query at this time
and keep results for 48 hours
The default is to merge overlapping regions in a query result, to keep these regions distinct click the following submit button. However this feature is available for only the region summary, bar graphs, and genome browser user track ouput formats. This feature is not currently available when the non-coding checkbox is selected.