Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across species. Accurate identification and classification of TEs present in a genome is an important step towards understanding their effects on genes and their role in genome evolution. We introduce TE-Learner, a framework based on machine learning that automatically identifies TEs in a given genome and assigns a classification to them. We present an implementation of our framework towards LTR retrotransposons, a particular type of TEs characterized by having long terminal repeats (LTRs) at their boundaries. We evaluate the predictive performance of our framework on the well-annotated genomes of Drosophila melanogaster and Arabidopsis thaliana and we compare our results for three LTR retrotransposon superfamilies with the results of three widely used methods for TE identification or classification: RepeatMasker, Censor and LtrDigest. In contrast to these methods, TE-Learner is the first to incorporate machine learning techniques, outperforming these methods in terms of predictive performance, while able to learn models and make predictions efficiently. Moreover, we show that our method was able to identify TEs that none of the above method could find, and we investigated TE-Learner’s predictions which did not correspond to an official annotation. It turns out that many of these predictions are in fact strongly homologous to a known TE.

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RESUMO -Avaliou-se a relação entre os testes complementares (teste hiposmótico, teste de termorresistência lento e teste de reação acrossômica) e os testes de avaliações convencionais (aspectos físicos e morfológicos) de sêmen bovino congelado/descongelado e os índices de prenhez. Os valores médios da motilidade espermática progressiva retilínea avaliados pelo teste de termorresistência foram de 53,48 (pós-descongelamento), 43,69 (60 minutos), 35,88 (120 minutos) e 33,04% (180 minutos) e a porcentagem de células reativas ao teste hiposmótico foi de 37,89%. Correlação positiva e de média intensidade foi encontrada para a motilidade espermática progressiva retilínea pós-descongelamento e o teste hiposmótico (0,21). Entretanto, a correlação da motilidade aos 180 minutos com o teste hiposmótico foi alta (0,64). A porcentagem de células que tiveram acrossoma reagido pós-descongelamento foi de 9,85%, apresentando correlações negativas de média e alta intensidade (-0,25 e -0,46, respectivamente) com a motilidade espermática progressiva retilínea pós-descongelamento e após 3 horas de incubação. Não houve correlação dos testes complementares e da motilidade pós-descongelamento com a taxa de gestação. Nenhum parâmetro considerado isoladamente serviu para avaliar a capacidade fertilizante do sêmen congelado/ descongelado. Palavras-chave: fertilidade, sêmen, testes complementares, touroRelationship between conception rates obtained by using bovine frozen semen and in vitro spermatic evaluation ABSTRACT -The objective of this study was to evaluate the relationship between complementary (hiposmotic, thermoresistance and acrosome reaction tests) and conventional evaluations (physical and morphologic aspects) of bovine frozen/ thawed semen and conception rates. Average values for spermatic motility evaluated by thermo-resistance test were of 53.48% (post-thawed), 43.69% (60 minutes), 35.88% (120 minutes) and 33.04% (180 minutes). The percentage of reactive cells observed for the hiposmotic test was 37.89%. Average intensity was observed for post-thawing spermatic motility, positively correlated to hiposmotic test (0.21). However, correlation between motility in the 180 minutes and hiposmotic test was high (0.64). The percentage of cells presenting post-thawing acrosome reaction was 9.85%, which was negative correlated to postthawing (-0.25) and after three hours of incubation (-0.46) spermatic motility. No correlation was observed for complementary tests and post-thawed motility and the conception rate. No one of the parameters evaluated in this study was individually able to indicate the fertilizing capacity of the frozen/thawed semen.