Finds putative bacteriocin open reading frames (ORFs) in a DNA sequence. BAGEL uses knowledge-based bacteriocin databases and motif databases to make the identification. It combines direct and indirect mining by looking at context genes. This tool integrates RNASeq data, promoter and terminator predictions. It can investigate the sequence of the surrounding region on the genome for genes that might encode proteins involved in biosynthesis, transport, regulation and/or immunity.
Provides a broad-spectrum pipeline. PepSAVI-MS is a pipeline for the screening and identification of cationic bioactive peptides from natural product sources. This platform is adaptable to any natural product source of peptides and can test against diverse physiological targets, including bacteria, fungi, viruses, protozoans, and cancer cells for which there is a developed bioassay.
A web app to find antimicrobial peptides as new infection therapeutics. MLAMP is developed using ML-SMOTE and grey pseudo amino acid composition. MLAMP obtains 0.4846 subset accuracy and 0.16 hamming loss. This prediction performance is better than iAMP-2L and CAMP. Users can submit a peptide sequence to the webserver and subsequently the webserver returns the predicted result in real time.
Identifies antimicrobial peptides (AMPs). Antilicrobial Peptide Scanner employs a deep neural network (DNN) classifier with convolutional and recurrent layers. It supports high-throughput screening experiments where wet-laboratory researchers want to conduct systematic virtual screenings of peptide libraries. This tool allows the prediction of antibacterial activity against specific species of bacteria.
Furnishes method for identifying antimicrobial peptides using word embedding with deep recurrent neural networks. This program is able to determine bacteriocins from protein sequences without using sequence similarity. This tool can represent protein sequences using Word2vec and utilizes a recurrent neural network (RNN) to distinguish bacteriocin between non-bacteriocin sequences.
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