Background: Although the development of sequencing technologies has provided a large number of protein sequences, the analysis of functions that each one plays is still difficult due to the efforts of laboratorial methods, making necessary the usage of computational methods to decrease this gap. As the main source of information available about proteins is their sequences, approaches that can use this information, such as classification based on the patterns of the amino acids and the inference based on sequence similarity using alignment tools, are able to predict a large collection of proteins. The methods available in the literature that use this type of feature can achieve good results, however, they present restrictions of protein length as input to their models. In this work, we present a new method, called TEMPROT, based on the fine-tuning and extraction of embeddings from an available architecture pre-trained on protein sequences. We also describe TEMPROT+, an ensemble between TEMPROT and BLASTp, a local alignment tool that analyzes sequence similarity, which improves the results of our former approach. Results: The evaluation of our proposed classifiers with the literature approaches has been conducted on our dataset, which was derived from CAFA3 challenge database. Both TEMPROT and TEMPROT+ achieved competitive results on $$F_{\max }$$F max , $$S_{\min }$$S min , AuPRC and IAuPRC metrics on Biological Process (BP), Cellular Component (CC) and Molecular Function (MF) ontologies compared to state-of-the-art models, with the main results equal to 0.581, 0.692 and 0.662 of $$F_{\max }$$F max on BP, CC and MF, respectively. Conclusions: The comparison with the literature showed that our model presented competitive results compared the state-of-the-art approaches considering the amino acid sequence pattern recognition and homology analysis. Our model also presented improvements related to the input size that the model can use to train compared to the literature methods.

Recently, several studies have been concerned with modeling the parenthood relationships between near duplicates in a set of images. Two images share a parenthood relationship if one is obtained by applying transformations to the other. However, this is not the only form of parenting that can exist among images. An image might be a composition created through the combination of the semantic information existent in two or more source images, establishing a relationship between the sources and the composite. The problem of identifying these relations in a set containing near-duplicate subsets of source and composition images is referred to as multiple parenting phylogeny. Thus far, researchers tackled this problem with a three-step solution: 1) separation of near-duplicate groups; 2) classification of the relations between the groups; and 3) identification of the images used to create the original composition. In this work, we extend upon this framework by introducing key improvements, such as better identification of when two images share content, and improved ways to compare this content. In addition, we also introduce a new realistic professionally created data set of compositions involving multiple parenting relationships. The method we present in this paper is properly evaluated through quantitative metrics, established for assessing the accuracy in finding multiple parenting relationships. Finally, we discuss some particularities of the framework, such as the importance of an accurate reconstruction of phylogenies and the method's behavior when dealing with more complex compositions.

Background: Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map contigs onto a reference genome. However, rearrangements that may exist between the query and reference genomes may result in incorrect scaffolds, if these rearrangements are not taken into account. Large-scale inversions are common rearrangement events in prokaryotic genomes. Even in draft genomes it is possible to detect the presence of inversions given sufficient sequencing coverage and a sufficiently close reference genome. Results: We present a linear-time algorithm that can generate a set of contig scaffolds for a draft genome sequence represented in contigs given a reference genome. The algorithm is aimed at prokaryotic genomes and relies on the presence of matching sequence patterns between the query and reference genomes that can be interpreted as the result of large-scale inversions; we call these patterns inversion signatures. Our algorithm is capable of correctly generating a scaffold if at least one member of every inversion signature pair is present in contigs and no inversion signatures have been overwritten in evolution. The algorithm is also capable of generating scaffolds in the presence of any kind of inversion, even though in this general case there is no guarantee that all scaffolds in the scaffold set will be correct. We compare the performance of sis, the program that implements the algorithm, to seven other scaffold-generating programs. The results of our tests show that sis has overall better performance. Conclusions: sis is a new easy-to-use tool to generate contig scaffolds, available both as stand-alone and as a web server. The good performance of sis in our tests adds evidence that large-scale inversions are widespread in prokaryotic genomes.