dbAMP

AMPfinder Genomic / Proteomic data mining approaches for the discovery of AMPs

AMPfinder is a simple, yet accurate, computational pipeline that processes either genomes and proteome sequences. The search for AMPs is based on alignment searching the existing antimicrobial peptide database and predicting on the feature model in amino acid sequence obtained from the translation of the original transcriptome sequence data.

AMPfinder is a free software tool that combines ORF prediction and accurately classification of the AMPs from protein or nucleotide data, which performs translation of the input transcriptome data by using Prodigal, and selects short sequences containing ORF and signal peptide cleavage sites. Then, DIAMOND was used for homology detection and machine learning prediction model were used to search for potential AMPs, in which case all known or potential motifs will be revealed and classified. Due to the combination of various search methods, AMPfinder searcher allows to obtain the most complete repertoire of AMPs for one or more transcriptomes in a short amount of time. Therefore, AMPfinder seems to be the most suitable tool for rapid screening of potential AMPs.

USE AMPfinder:

You can paste a DNA or Protein sequence or several sequences with FASTA format into the field below: Upload FASTA sequence file:

Upload a plain text file containing DNA or protein sequence(s) in FASTA format (20 Mb limit). The file can contain more than one FASTA formatted sequence, such as assembly contigs or multiple proteins. Each file will be treated as a single sample.

Select Data Type:

DNA Sequence

Protein Peptides

Enter a GenBank accession(s):

Nucleotide sequences will undergo ORF calling to generate predicted protein sequences.
Examples: JN420336.1, AY123251.1, HQ451074.1, AL123456

Select Criteria:

Predictive score > 90

Predictive score > 70

Model Taxonomy:

* Enter Your Email:

Mandatory, where results will be sent to.

ID:

optional, your given name of the project title.