Expedited batch processing and analysis of transposon insertions
<p>Abstract</p> <p>Background</p> <p>With 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 v...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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BMC
2011-11-01
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| Series: | BMC Research Notes |
| Online Access: | http://www.biomedcentral.com/1756-0500/4/482 |
| _version_ | 1823999564010487808 |
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| author | Smith Jeremy D Ray David A |
| author_facet | Smith Jeremy D Ray David A |
| author_sort | Smith Jeremy D |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>With 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.</p> <p>Findings</p> <p>In 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.</p> <p>Conclusions</p> <p>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.</p> |
| first_indexed | 2024-12-18T17:46:21Z |
| format | Article |
| id | doaj.art-a8f8855c0236418fa537165cc57cc2d2 |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-12-18T17:46:21Z |
| publishDate | 2011-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-a8f8855c0236418fa537165cc57cc2d22022-12-21T20:59:00ZengBMCBMC Research Notes1756-05002011-11-014148210.1186/1756-0500-4-482Expedited batch processing and analysis of transposon insertionsSmith Jeremy DRay David A<p>Abstract</p> <p>Background</p> <p>With 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.</p> <p>Findings</p> <p>In 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.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1756-0500/4/482 |
| spellingShingle | Smith Jeremy D Ray David A Expedited batch processing and analysis of transposon insertions BMC Research Notes |
| title | Expedited batch processing and analysis of transposon insertions |
| title_full | Expedited batch processing and analysis of transposon insertions |
| title_fullStr | Expedited batch processing and analysis of transposon insertions |
| title_full_unstemmed | Expedited batch processing and analysis of transposon insertions |
| title_short | Expedited batch processing and analysis of transposon insertions |
| title_sort | expedited batch processing and analysis of transposon insertions |
| url | http://www.biomedcentral.com/1756-0500/4/482 |
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