Abstract
BackgroundWith advances in sequencing technology, greater and greater amounts of eukaryotic genome data are becoming available. Often, large portions of these genomes consist of transposable elements, frequently accounting for 50% or more in vertebrates. Each transposable element family may have thousands or tens of thousands of individual copies within a given genome, and therefore it can take an exorbitant amount of time and effort to process data in a meaningful fashion.FindingsIn order to combat this problem, we developed a set of bioinformatics techniques and programs to streamline the analysis. This includes a unique Perl script which automates the process of taking BLAST, Repeatmasker and similar data to extract and manipulate the hit sequences from the genome. This script, called Process_hits uses an object-oriented methodology to compile all hit locations from a given file for processing, organize this data into useable categories, and output it in multiple formats.ConclusionsThe program proved capable of handling large amounts of transposon data in an efficient fashion. It is equipped with a number of useful sub-functions, each of which is contained within its own sub-module to allow for greater expandability and as a foundation for future program design.
Highlights
With advances in sequencing technology, greater and greater amounts of eukaryotic genome data are becoming available
The program proved capable of handling large amounts of transposon data in an efficient fashion
It is equipped with a number of useful sub-functions, each of which is contained within its own sub-module to allow for greater expandability and as a foundation for future program design
Summary
With advances in sequencing technology, greater and greater amounts of eukaryotic genome data are becoming available. RepeatMasker identifies and masks transposable elements using a known library, while BLAST will output matches to query sequences based on the quality of the match. These tools include a unique set of Perl scripts which automate the process of taking BLAST, Repeatmasker or similar data, locating the hit sequence, and exporting these sequences with unique IDs to a new FASTA file.
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