Schema for Placental Chain/Net - Placental Genomes, Chain and Net Alignments
  Database: mm10    Primary Table: chainFelCat9    Row Count: 2,789,235   Data last updated: 2018-03-15
Format description: Summary info about a chain of alignments
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 607smallint(5) unsigned Indexing field to speed chromosome range queries.
score 13727double score of chain
tName chr1varchar(255) Target sequence name
tSize 195471971int(10) unsigned Target sequence size
tStart 3007228int(10) unsigned Alignment start position in target
tEnd 3007939int(10) unsigned Alignment end position in target
qName chrB3varchar(255) Query sequence name
qSize 149751809int(10) unsigned Query sequence size
qStrand +char(1) Query strand
qStart 137234848int(10) unsigned Alignment start position in query
qEnd 137235516int(10) unsigned Alignment end position in query
id 993581int(10) unsigned chain id

Connected Tables and Joining Fields
        mm10.chainFelCat9Link.chainId (via chainFelCat9.id)
      mm10.netFelCat9.chainId (via chainFelCat9.id)

Sample Rows
 
binscoretNametSizetStarttEndqNameqSizeqStrandqStartqEndid
60713727chr119547197130072283007939chrB3149751809+137234848137235516993581
60713534chr119547197130125913014185chrF285752456-75677578756797561021972
60811068chr119547197130740163074335chrF285752456-75696586756969101396169
98381005chr119547197130945447172812chrF285752456-7569912679076609174
60811496chr119547197131451093145405chrD1117648028+16715145167155011333590
60928223chr119547197131468963147334chrA1242100913+132222552132223017203527
6099728chr119547197131469133147121chrB3149751809+98408341984085581577602
6099785chr119547197131469133147179chrA1242100913+15281722152820211570332
60925825chr119547197132159743217027chrA3143202405+2703900827040068248794
60927010chr119547197132160193216991chrB1208212889+5406745154068432225173

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Placental Chain/Net (placentalChainNet) Track Description
 

Description

Chain Track

The chain track shows alignments of mouse (Dec. 2011 (GRCm38/mm10)/mm10) to other genomes using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both mouse and the other genome simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.

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 other assembly or an insertion in the mouse 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 other 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.

Net Track

The net track shows the best mouse/other chain for every part of the other genome. It is useful for finding orthologous regions and for studying genome rearrangement. The mouse sequence used in this annotation is from the Dec. 2011 (GRCm38/mm10) (mm10) assembly.

Display Conventions and Configuration

Multiple species are grouped together in a composite track. In the display and on the configuration page, an effort was made to group them loosely into "clades." These groupings are based on the taxonomic classification at NCBI, using the CommonTree tool. Some organisms may be pulled from a larger group into a subgroup, to emphasize a relationship. For example, members of an Order may be listed together, while other organisms in the same Superorder may be grouped separately under the Superorder name.

Chain Track

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.

Net Track

In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth.

In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement.

Individual items in the display are categorized as one of four types (other than gap):

  • Top - the best, longest match. Displayed on level 1.
  • Syn - line-ups on the same chromosome as the gap in the level above it.
  • Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation.
  • NonSyn - a match to a chromosome different from the gap in the level above.

Methods

Chain track

Transposons that have been inserted since the mouse/other split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single mouse chromosome and a single chromosome from the other genome 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.

See also: lastz parameters and other details (e.g., update time) and chain minimum score and gap parameters used in these alignments.

Net track

Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged.

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.

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 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. 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