Finding Exact and Solo LTR-Retrotransposons in Biological Sequences Using SVM

finding exact and solo ltr-retrotransposons in biological sequences using svm

finding repetitive subsequences in genome is a challengeable problem in bioinformatics research area. a lot of approaches have been proposed to solve the problem, which could be divided to library base and de novo methods. the library base methods use predetermined repetitive genome’s subsequences, where library-less methods attempt to discover repetitive subsequences by analytical approaches. ...

LTR Retrotransposons in Fungi

Transposable elements with long terminal direct repeats (LTR TEs) are one of the best studied groups of mobile elements. They are ubiquitous elements present in almost all eukaryotic genomes. Their number and state of conservation can be a highlight of genome dynamics. We searched all published fungal genomes for LTR-containing retrotransposons, including both complete, functional elements and ...

Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons

Retrotransposons with long terminal repeats (LTR) form a significant proportion of eukaryotic genomes, especially in plants. They have gag and pol genes and several regulatory regions necessary for transcription and reverse transcription. We searched for potential quadruplex-forming sequences (PQSs) and potential triplex-forming sequences (PTSs) in 18 377 full-length LTR retrotransposons collec...

Non-LTR retrotransposons and microsatellites

The human genome is laden with both non-LTR (long-terminal repeat) retrotransposons and microsatellite repeats. Both types of sequences are able to, either actively or passively, mutagenize the genomes of human individuals and are therefore poised to dynamically alter the human genomic landscape across generations. Non-LTR retrotransposons, such as L1 and Alu, are a major source of new microsat...

Mining Biological Repetitive Sequences Using Support Vector Machines and Fuzzy SVM

Structural repetitive subsequences are most important portion of biological sequences, which play crucial roles on corresponding sequence’s fold and functionality. Biggest class of the repetitive subsequences is “Transposable Elements” which has its own sub-classes upon contexts’ structures. Many researches have been performed to criticality determine the structure and function of repetitiv...

Automated search for LTR retrotransposons