A. gambiae Chain Track Settings
 
A. gambiae (Feb. 2003 (IAGEC MOZ2/anoGam1)) Chained Alignments   (All Comparative Genomics tracks)

Display mode:   

Color track based on chromosome:  on off

Filter by chromosome (e.g. chr10):

Display data as a density graph:

View table schema
Data last updated: 2006-12-05

Description

This track shows alignments of A. gambiae (anoGam1, Feb. 2003 (IAGEC MOZ2/anoGam1)) to the D. melanogaster genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both A. gambiae and D. melanogaster simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. The A. gambiae sequence is from the MOZ2 assembly.

The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the A. gambiae assembly or an insertion in the D. melanogaster assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the D. melanogaster genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.

In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment.

Display Conventions and Configuration

By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome.

To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome.

Methods

The A. gambiae/D. melanogaster genomes were aligned with blastz and converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single A. gambiae chromosome and a single D. melanogaster chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:

 ACGT
A91-90-25-100
C-90100-100-25
G-25-100100-90
T-100-25-9091

Chains scoring below a threshold were discarded; the remaining chains are displayed in this track.

Credits

Blastz was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison.

Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program.

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

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

References

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

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. PMID: 14500911; PMC: PMC208784

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. PMID: 12529312; PMC: PMC430961