Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family.

Expansins, which are plant cell wall loosening proteins associated with cell growth, have been identified as a multigene family. Plant expansin proteins are an important family that functions in cell growth and many of developmental processes including wall relaxation, fruit softening, abscission, seed germination, mycorrhiza and root nodule formation, biotic and abiotic stress resistance, invasion of pollen tube stigma and organogenesis. In addition, it is thought that increasing the efficiency of plant expansin genes in plants plays a significant role, especially in the production of secondary bioethanol. When the studies on the expansin genes are examined, it is seen that the expansin genes are a significant gene family in the cell wall expansion mechanism. Therefore, understanding the efficacy of expansin genes is of great importance. Considering the importance of this multigene family, we aimed to create a comprehensively informed database of plant expansin proteins and their properties. The expansin gene family database provides comprehensive online data for the expansin gene family members in the plants. We have designed a new website accessible to the public, including expansin gene family members in 70 plants and their features including gene, coding and peptide sequences, chromosomal location, amino acid length, molecular weight, stability, conserved motif and domain structure and predicted three-dimensional architecture. Furthermore, a deep learning system was developed to detect unknown genes belonging to the expansin gene family. In addition, we provided the blast process within the website by establishing a connection to the NCBI BLAST site in the tools section. Thus, the expansin gene family database becomes a useful database for researchers that enables access to all datasets simultaneously with its user-friendly interface. Our server can be reached freely at the following link (http://www.expansingenefamily.com/).

bHLHDB: A next generation database of basic helix loop helix transcription factors based on deep learning model.

The basic helix loop helix (bHLH) superfamily is a large and diverse protein family that plays a role in various vital functions in nearly all animals and plants. The bHLH proteins form one of the largest families of transcription factors found in plants that act as homo- or heterodimers to regulate the expression of their target genes. The bHLH transcription factor is involved in many aspects of plant development and metabolism, including photomorphogenesis, light signal transduction, secondary metabolism, and stress response. The amount of molecular data has increased dramatically with the development of high-throughput techniques and wide use of bioinformatics techniques. The most efficient way to use this information is to store and analyze the data in a well-organized manner. In this study, all members of the bHLH superfamily in the plant kingdom were used to develop and implement a relational database. We have created a database called bHLHDB (www.bhlhdb.org) for the bHLH family members on which queries can be conducted based on the family or sequences information. The Hidden Markov Model (HMM), which is frequently used by researchers for the analysis of sequences, and the BLAST query were integrated into the database. In addition, the deep learning model was developed to predict the type of TF with only the protein sequence quickly, efficiently, and with 97.54% accuracy and 97.76% precision. We created a unique and next-generation database for bHLH transcription factors and made this database available to the world of science. We believe that the database will be a valuable tool in future studies of the bHLH family.