MAK

MAK analyzes miniature inverted-repeat transposable elements (MITEs) by automating retrieval and positional characterization of family members to identify anchor elements linking MITEs to autonomous transposable element families and to discover novel transposons.

Key Features:

• Automated family member retrieval: Retrieves MITE family member sequences automatically for comparative analysis.
• Genomic position reporting: Reports precise positions of MITE copies relative to neighboring genes to characterize genomic context.
• Anchor element identification: Identifies anchor elements that connect MITE families with known transposable element (TE) families.
• Detection of TIRs and transposase-like coding regions: Detects terminal inverted repeats (TIRs) and coding regions similar to transposases in candidate autonomous elements.
• Genetic algorithm-based inference: Employs robust genetic algorithms derived from transposable element principles to infer relationships between MITEs and autonomous TEs.
• Novel transposon discovery: Identified novel transposon families Math and Kid belonging to the IS5/Harbinger/PIF superfamily.

Scientific Applications:

• Genomic context and regulatory impact analysis: Enables study of MITE insertion positions relative to genes to assess potential regulatory impacts.
• Validation of autonomous element hypotheses: Facilitates validation of proposed autonomous elements via detection of TIRs and transposase-like coding regions.
• Evolutionary relationship inference and discovery: Supports inference of evolutionary links between MITE families and known TE families and discovery of novel transposons such as Math and Kid (IS5/Harbinger/PIF).

Methodology:

MAK leverages structural characteristics and genetic principles of transposable elements and employs genetic algorithms to retrieve family member sequences, report positions relative to neighboring genes, identify anchor elements, and detect TIRs and coding regions similar to transposases.