A package for the extension of repetitive DNA sequences
RepeatAfterMe is an experimental package containing (currently) a single tool called RAMExtend. RAMExtend employs a method for extending a multiple sequence alignment (MSA) that represents a fragment of a larger repetitive sequence found in a given genome. The input MSA is treated as an immutable core while the flanking sequences are used to extend the MSA and generate a left/right consensus extension for the original core.
The extension algorithm is an enhanced version of the RepeatScout approach developed by Alkes Price, Neil Jones and Pavel Pevzner (See history below). Unlike the original RepeatScout program this tool may be used on complete genome sequences. In addition it has been re-written to use custom scoring matrices, and affine gap penalties.
An improved de novo tool is envisioned and will be made available in the new future.
Robert Hubley 2022 Institute for Systems Biology
The tool minimally requires two input files. The first is a file the core alignment to extend from. Ranges are supplied in the form of a modified BED-6 format:
BED-6 field name : RAMExtend use
field-1:chrom : sequence identifier
field-2:chromStart: lower aligned position ( 0 based )
field-3:chromEnd : upper aligned position ( 0 based, half open )
field-4:name : left extendable flag ( 0 = no, 1 = yes )
field-5:score : right extendable flag
field-6:strand : strand ( '+' = forward, '-' = reverse )
The fields are tab separated. Coordinates are zero-based, half-open. The 'extendable?' flags are used to limit the use of individual sequences in the left or right extension phases. This is useful when sequences in the core MSA are not of uniform length.
The second input file is the genome itself in 2bit format. This is where the tool extracts the flanking regions using the identifiers provided in the BED file.
For example:
./RAMExtend -ranges test/extension-test2.tsv -twobit test/extension-test2.2bit
There are additional options that are displayed if no options are specified.
The genesis for this project was with the great work by Alkes Price, Neil Jones and Pavel Pevzner. They developed a method for automatically extending aligned sequences ( abundant exact words ) allowing for the development of a dynamic multiple alignment. The details of their method are described in the following paper:
Price A.L., Jones N.C. and Pevzner P.A. 2005. De novo identification of repeat families in large genomes. To appear in Proceedings of the 13 Annual International conference on Intelligent Systems for Molecular Biology (ISMB-05). Detroit, Michigan.
One of the drawbacks for RepeatScout is the simple scoring system used by the program ( Match/Mismatch/Gap ). It was our initial goal to simply augment the RepeatScout package with custom matrix support and full affine gap penalties. As work progressed and the possibilities of further enhancing the code became clear it was decided that a new project should be created for this effort. RepeatAfterMe is designed as an experimental workbench for the application of this powerful extension algorithm to various types of aligned cores (kmers, alignment fragments etc).