BLAT search

You can do a BLAT (BLAST-like Alignment Tool) search from a user-specified sequence, feature, alignment, or region of interest, of a sequence up to 8 kb in length.

• User-specified sequence: Select BLAT from the Tools menu in the main menubar, and enter the sequence.
• Features: Right-click on the feature in the track and select Blat sequence from the pop-up menu. The BLAT input sequence is the section of the reference genome defined by the feature start and end bounds.
• Alignments: Right-click on the aligned read and select Blat read sequence from the pop-up menu. Note that in this case, the BLAT input sequence is the read sequence. It is not the sequence of the reference genome where the read was aligned.
• Regions of Interest (ROI): After creating a region of interest, click on the region's red bar and select Blat sequence from the pop-up menu. The BLAT input sequence is the sequence of the reference genome defined by the region bounds. 

The default search engine is the BLAT server hosted at the UCSC Genome Browser. UCSC's BLAT search supports most UCSC derived genomes including human and mouse genomes. Change to use a different BLAT server in Advanced Preferences.

BLAT Feature Track

Each query sequence appears as a new Blat feature track in the lower panel of IGV's display. The Screenshot (2015.04.01) shows five different Blat feature tracks for the following sequences:

1. Red highlighted read
2. Blue highlighted RNA-Seq read spanning an intron
3. An exon feature
4. An ROI covering an intronic region
5. An ROI spanning a region covering examples a–d.

Manipulate this track just like other feature tracks as outlined in the Feature Tracks section of the Pop-up Menus page.

• Each search item adds a new Blat feature track.
• Blat features display aligned regions as rectangles and gaps in alignments with lines.
• The Blat features change opacity depending on alignment score from dark blue to light blue. 
• The Blat feature marks directionality relative to the original search sequence as displayed by IGV, from left to right, with arrowheads.
• Expanded or Collapsed views of the Blat feature track labels the search feature YourSeq. You cannot alter this label but can rename the feature track.

BLAT Results Panel

Results are presented in a new window that displays the query sequence, location of hits, match score, and other metrics as shown in the Screenshot (2015.04.01). Hits are listed in descending order of alignment score.

For the example hit highlighted in the Screenshot above, the original search sequence is returned as the top hit. The read used in the search was an aligned RNA-Seq read spanning an intron (example b), which the BLAT results show is a singly gapped alignment as indicated by the 1 under the column T gap count.

• Each BLAT search gives a separate results panel.
• Once a results window is closed, you cannot reopen it.
• Click on a row in the results panel to navigate to the selected result locus. IGV centers the Blat feature on the display.

For example, for ROI2 (marked 1 above), clicking on the second hit in the results panel (marked 2 in Screenshot below) navigates the view away from chromosome 19 to the hit locus on chromosome 22 (marked 3). This same region contains a hit for example c, a BLAT search done with an exon feature. Because the exon feature has a higher alignment score than ROI2, its Blat feature is shaded darker.