Description

This track indicates any pair of exactly identical sequence for the 17 Oct 2024 Lissotriton helveticus/GCA_964261635.1_aLisHel1.1 genome assembly.

There may be two tracks in this composite collection:

Gap Overlaps - Paired exactly identical sequence on each side of a gap
Tandem Dups - Paired exactly identical sequence survey over entire genome assembly

The Gap Overlaps is thus a subset of the full Tandem Dups track.

This investigation began when an unusual number of paired sequences around gaps was noticed during the mouse strain sequencing project. This naturally raised the question, how common is this feature, and what type of assemblies can it be found in.

The Gap Overlaps track indicates any pair of exactly identical sequence on each side of gaps. Where a gap is any run of N's, including a single N. The end of an upstream sequence before the gap is duplicated exactly at the beginning of the downstream sequence following the gap in the assembly.
Data in track: Item count: 48; Bases covered: 29,700.

The Tandem Dups track is a similar survey over the entire genome assembly. The separation gap between these paired sequences can range from 1 base up to 20,000 bases.
Data in track: Item count: 1,460,718; Bases covered: 463,878,635.

Methods

The Gap Overlap duplicate sequences were found by extracting 1,000 bases before and after each gap and aligned to each other with the blat command:

  blat -q=dna -minIdentity=95 -repMatch=10 upstreamContig.fa downstreamContig.fa

Filtering the PSL output for a perfect match, no mis-matches, and therefore of equal size matching sequence, where the alignment ends exactly at the end of the upstream sequence, and begins exactly at the start of the downstream sequence.

The Tandem Dups paired sequences were found with the following procedure:

Generate 29 base kmers for the entire genome, allow only kmers with bases: A C T G, no N's allowed.
Pair up identical kmers with at least one base separation and up to 20,000 bases separation.
Collapse overlapping kmer pairs when they are the same size of sequence and the same spacing between the pairs. This procedure preserves the definition of duplicated identical pairs.
The resulting pairs can now be longer sequences with smaller separation then the constituent pairs
Final result selects sizes of 30 bases or more for the size of the paired sequence, and at least one base remaining as a separation gap.
Collapsed pairs that close the gap are discarded. They appear to indicate simple repeat sequences when this happens. It would be interesting to have this result available, but that is not available at this time.

The reason for starting with 29 base sized pairs and then selecting results of at least 30 base sized pairs results in a reasonable number of 30 base pairs. If the procedure starts with 30 base sized pairs, it produces way too many 30 base kmer pairs for a reasonable count.

Credits

Thank you to Joel Armstrong and Benedict Paten of the Computational Genomics Lab at the U.C. Santa Cruz Genomics Institute for identifying this characteristic of genome assemblies.

The data and presentation of this track were prepared by Hiram Clawson, U.C. Santa Cruz Genomics Institute

Description

Methods

See Also

Credits