GALA Help: Compound Query Operations

Not

NOT finds all of the nucleotides in the chromosome that are NOT included in the query results. If the original query does not include anything from a chromosome, that chromosome will be skipped.

(In this illustration '|' marks the ends of the sequence.)

query 1: |     ----             --------           -----------     ---       |

results: |-----    -------------        -----------           -----   -------|

Restrict region size

This option filters out all regions that are smaller or larger than the specified length. No trimming is done; a region is either retained or rejected.

In this example the user chose "greater than or equal to 6".

query 1:       ----             --------           -----------     ---

results:                        --------           -----------

Get aligning coordinates from pairwise alignments for ..

This option uses pairwise alignments to find similar regions in other species to the query results.

In this example the mouse coordinates were requested for a query done on human.

query:     --------------      -----------           ----------------

pairwise alignment human vs mouse
human         **************                   *****************************

mouse         **************                   *****************************

results:      -----------                            ----------------

These results are then ordered by chromosome and start point and displayed in the GALA page with the same release.

Union

UNION finds all regions that are covered by either of the queries.

query 1:    ---       -----            ------                   ---------
query 2:       ----     ----                  ---

results:    -------   ------           ------ ---               ---------

Intersection

INTERSECTION finds regions that overlap. The difference between the available choices lies in how the returned region is defined.

Using "INTERSECTION"

query 1:   --------------          ----    ------------------
query 2:         ---------------                ------             -------

results:   ---------------------           ------------------

Using "INTERSECTION and trim regions"

query 1:   --------------          ----    ------------------
query 2:         ---------------                ------             -------

results:         --------                       ------

Using "INTERSECTION returning ranges from the earlier query that overlap anything in the later query"

query 1:   --------------          ----    ------------------
query 2:         ---------------                ------             -------

results:   --------------                  ------------------

Using "INTERSECTION returning ranges from the later query that overlap anything in the earlier query"

query 1:   --------------          ----    ------------------
query 2:         ---------------                ------             -------

results:         ---------------                ------

Subtraction

Subtraction removes one query's regions from another query. The user can specify the direction of the subtraction, and whether a region that is overlapped by the other query should be completely removed ("whole region"), or only the overlapping sections should be removed.

Subtracting the earlier minus the later query. (The terms "earlier" and "later" refer to the queries' relative positions in the history list.) Result 1 is from selecting "whole regions", while Result 2 is from "only overlapping segments".

query 1:      ----------      -------             -------------------
query 2:         ---------------         ------                           ----

Result 1:                                         -------------------
Result 2:     ---               -----             -------------------

The same two queries, only subtracting later minus earlier.

query 1:      ----------      -------             -------------------
query 2:         ---------------         ------                           ----

Result 1:                                ------                           ----
Result 2:               ------           ------                           ----

Proximity

Proximity returns regions from the first query that either lie within a specified distance from some region in the second query, or lie farther than the specified distance from all regions in the second query. (Note that the regions' closest endpoints are used; i.e. their minimum distance is measured and compared against the user's threshold.) Also, if the regions in the second query are genes, then the search can be limited to just the areas upstream or downstream of those genes.

Return regions from query 1 within 500 bp of a region in query 2. (Each '-' will represent 100 bp in these diagrams.)

query 1:    ---          -----       --         ---            --
query 2:                 -------------------                             -----

search:             *****************************                   ***************

results:                 -----       --         ---

Return regions from query 1 that lie more than 500 bp from all regions in query 2.

query 1:    ---          -----       --         ---            --
query 2:                 -------------------                             -----

search:  ***********                             *******************               *****

results:    ---                                                --

Return regions from query 1 that lie within 500 bp upstream of a gene in query 2.

query 1:    ---          -----       --         ---            --
query 2:                 <------------------                       ---->

search:                                     *****             *****

results:                                        ---            --

Cluster

Cluster finds regions from one query that have N regions from a second query within M bp of them, where the user enters the numbers for N and M. The regions that are returned are the qualifying ones from the first query, with M bp added to both ends. If the same query is compared with itself, each region will always count as being within M bp of itself, so be sure to request N of at least 2.

Return regions from query 1 with at least 3 regions from query 2 within 10 bp.

query 1:    ----------                          --------------

search:  ***********************      **********************************

query 2:               ---  -----                 -----           --- ---

results:                              ----------------------------------

Return regions from query 1 with at least 2 regions from that same query (i.e. at least one other region) within 10 bp.

query 1:                  ---------        ---------                      ---

search:         *****************************
                                 *****************************  ***********************

query 1:                  ---------        ---------                      ---

results:        ----------------------------------------------