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 was developed at
Miller Lab at Pennsylvania State University by
Bob Harris.
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
Harris RS.
Improved pairwise alignment of genomic DNA.
Ph.D. Thesis. Pennsylvania State University, USA. 2007.
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.
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