β-LacFamPred: An online tool for prediction and classification of β-Lactamases in class, subclass and family
Created by the Compuational Biology Group at University of Delhi, South Campus
Developer: Deeksha Pandey (deeksha.pandey.biophysics@south.du.ac.in)
Webserver Available at: http://www.proteininformatics.org/mkumar/blacfampred/
β-lactams are a broad class of antimicrobial agents with a high degree of safety profile. These two factors made them the most widely used class of antimicrobial agents in clinical, agricultural, and veterinary setups. The widespread use of β-lactams has induced extensive spread of β-Lactamases (BLs) that degrade β-lactam antibiotics. Further, the development of newer generations of β-lactams led to the evolution of a highly diverse group of BLs. On the basis of amino acid sequence homology, BLs are categorized through classes A to D in the Ambler system. The Bush–Jacoby system groups BLs through 1 to 4 on the basis of substrate hydrolysis and inhibitor profile. Traditional methods of determining the hydrolytic profile of BLs and their classification is time-consuming, hence we developed a Hidden Markov Models (HMM) based in-silico method, named as β-LacFamPred, for prediction and annotation of Ambler’s class, subclass, and 95 families of BLs.
The following dependencies are for use of the β-lacFamPred workflow scripts. If you wish to use your own workflow, then copy the HMM files in β-lacFamPred using the link http://www.proteininformatics.org/mkumar/blacfampred/COMBINED/PROTEIN/ in case of protein or nucleotide http://www.proteininformatics.org/mkumar/blacfampred/COMBINED/NUCLEOTIDE/ to the desired location on your server/computer for use with your installation of HMMER.
HMMER download and install as standalone using link: http://hmmer.org/download.html
workflow scripts were tested on GNU Bash v4.3.11 and later scripts were tested on Ubuntu, Linux, Centos and Mac OS (no testing was performed for windows operating systems)
-
unpack "blacfampred_standalone.tar.gz"
tar -xvzf blacfampred_standalone.tar.gz
cd blacfampred_standalone/
-
Install the HMMER v3.1 package to run HMMSCAN & NHMMSCAN from the blacfampred_standalone folder.
step1: uncompress: uncompress hmmer-3.1b2.tar.gz
step2: unpack: tar -xvzf hmmer-3.1b2.tar
step3: move into new directory: cd hmmer-3.1b2
step4: configure: ./configure
step5: build: make
step6: automated tests: make check
step7: automated install: make install
- Define the complete path of installed HMMER for 'HMMSCAN for protein sequences' and 'NHMMSCAN for nucleotide sequences' for scanning of AR genes.