GALA query page

GALA: Genome Alignment and Annotation database on Human April 2003 Freeze

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.
For text boxes:
match exact case onlymatch upper- or lower-case

Genes and Gene Predictions
all genes (default set, Locus Link Genes)
Other fields for genes ShowHide

EST and mRNA ShowHide the fields for this category

Comparative Genomics ShowHide the fields for this category
Multiple Alignments
The alignments were generated using humor for human, mouse, rat alignments and multiz for other multiple alignments Download the alignment files from UCSC Genome Browser
Query all multiple alignmentsonly regions that align in all species
Species: human vs Score (range between 0 and 2938272) to

Pairwise Alignments
The source of the alignment data is the UCSC Genome Browser and Penn State - Bioinformatics Group
Query all alignments
Species: human vs
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
All DNA aligned with both mouse and rat
All nonrepetitive DNA aligned with both mouse and rat
All ancestral repetitive DNA aligned with both mouse and rat
All simple repetitive DNA aligned with both mouse and rat

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 .
Score(scale 0.00 to 0.00) greater than or equal to and less than or equal to
Regulatory potential scores based on multiple alignments
Score(scale -0.11 to 0.27) greater than or equal to and less than or equal to

Mouse Cons
The source of the Mouse Cons is UCSC Genome Browser
Score (scale 0.000-8.000) greater than or equal to and less than or equal to

Variation and Repeats ShowHide the fields for this category

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)
only binding sites conserved in hg15Mm3Rn3 cutoff used was 0

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 ShowHide

Mapping and Sequencing ShowHide the fields for this category

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.

Show all of form

Output

Format of output FAQ about formats

Index pages	region summary gene summary
Graphical displays	UCSC Genome Browser user track Laj alignment viewer text alignment Mulan rVista zPicture bar graphs
Computer readable formats	text list BED format 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.