Alignment Track Settings
 
Alternate mouse strains, alignments to reference genome   (Alternate strains)

This track is part of a parent called 'Alternate strains'. To show other tracks of this parent, go to the Alternate strains configuration page.

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Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query
Draw a vertical green line where query has a polyA tail insertion
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Data last updated: 2012-11-09

Description

This track shows alternate mouse strain sequences indicated by the GRC (Genome Reference Consortium) mapped to the GRCm38 (mm10) reference sequence in an effort to provide the best possible reference assembly for the mouse genome. The GRC does this by generating multiple representations, alternate loci, for regions that are too complex to be represented by a single path. This allows users who are interested in a specific locus to get an improved representation without affecting users who need chromosome coordinate stability.

Alignment

The Alignment track is the PSL representation of the lastz chained alignments of the alternate strain sequences to their mapped location on the reference sequence. This PSL representation allows the side-by-side alignment to be viewed. It was created from the lastz chained alignments using the chainToPsl kent source utility. This track follows the display conventions for PSL alignment tracks. Alignments are displayed in black and, depending on the track configuration settings, may be interspersed with vertical orange lines.

Alternate strains

Items in the Alt. strains track indicate where the alternate mouse strain sequences map to the reference genome location. Clicking on an item in this track will display the detail page for that item, including a link to the nucleotide sequence at NCBI/Genbank for the alternate mouse strain. Data points in this track are always displayed in red.

The locations of the Alternate strains were established by NCBI and specified in the alt_scaffold_placement.txt files at, for example, strain NOD_ShiLtJ:
GRCm38.p1/NOD_ShiLtJ/alt_scaffolds/alt_scaffold_placement.txt. Note that each alternate strain has a unique directory at Mus_musculus/GRCm38.p1/.

Credits

Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison.

The axtChain program was developed at the University of California Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.

The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent.

The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent.

References

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26.

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7.