CryGetter: a tool to automate retrieval and analysis of Cry protein data

Abstract

BackgroundFor many years, the use of chemical agents to control crop pests has been degrading the environment, bringing problems to humans and all living things. An alternative to deal with the pests is the use of biopesticides, biological agents capable of controlling these harmful organisms. One kind of biopesticide is Bacillus thuringiensis, a Gram-positive bacterium that synthesizes a protein that, when ingested by the pests, kills them and does not harm other species.ResultsSince the economical importance of Bacillus thuringiensis and its proteins significance, this work presents a software tool, called CryGetter, that is capable of retrieving data related to these proteins, store it and present it in a user friendly manner. The tool also aims to align the protein sequences and generate reports containing some statistical data concerning the alignments that were made.ConclusionsCryGetter was created to help researchers of Bacillus thuringiensis and its proteins to speed up their data retrieval and analysis, allowing them to generate more accurate results. In this sense, the tool circumvents the error prone task of manually getting all the necessary data and processing them in various software systems to get the same result as CryGetter gets in a unique semiautomatic environment.

No More Tears: Mining Sequencing Data for Novel Bt Cry Toxins with CryProcessor

“…We performed the verification of how accurately CryProcessor predicts the positions of the domains among 3d-Cry toxin sequences. To carry out this procedure, we summarized the coordinates of start and stop positions of the domains obtained from CryProcessor and CryGetter, respectively [11]. We then calculated the mean differences between corresponding positions.…”

“…Manually curated models allow users to obtain the positions of the domains in analyzed toxins. CryGetter [11] possesses this ability only in terms of gathering Cry toxin data from Bt nomenclature, but it does not provide the opportunity to extract domains from the arbitrary query.…”

“…For now, there is no instrument that can possibly carry out this procedure. Manual queries using the Pfam database lack the potency to handle thousands of sequences while CryGetter [11] contains layout information only for a predefined number of toxins. Therefore, CryProcessor gives users a unique opportunity to obtain domain layout from potentially unlimited datasets.…”

“…For HMM model compilation, sequences from CryGetter (v1.03, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, São Paulo, Brazil, 2016) [11] technical data were used. All four models (one for full-size toxins and one per each domain within mature Cry toxins) were made of the CryGetter-provided dummies with the hmmbuild utility and tested independently with 30% identity threshold to assess the accuracy of the search.…”

“…For now, there is no specific instrument capable of generating domain structures among the sequences of 3d-Cry toxins. The only tool, which provides data for domain boundaries of Cry toxins, is CryGetter [11]. Nonetheless, it provides data only for a limited predefined set of proteins.…”