Package: il6pred
il6pred##A method for predicting and designing IL-6 inducing peptides.IntroductionIL6Pred is developed for predicting, designing and scanning interleukin-6 inducing peptides. Please read and cite the following paper for complete information including algorithm behind il6Pred.Models:In this program, one model has been incorporated for predicting interleukin-6 inducing peptides. The model is trained on IL-6 inducing and non-inducing peptides.Modules/Jobs:This program implement three modules (job types); i) Predict: for predicting interleukin-6 inducing peptides, ii) Design: for generating all possible peptides and computing interleukin-6 inducing potential (score) of peptides, iii) Scan: for creating all possible overlapping peptides of given length (window) and computing interleukin-6 inducing potential (score) of these overlapping peptides.ReferenceDhall A, Patiyal S, Sharma N, Usmani SS, Raghava GPS (2020) Computer-aided prediction and design of IL-6 inducing peptides: IL-6 plays a crucial role in COVID-19.Brief Bioinform. 22(2):936-945.Web Serverhttps://webs.iiitd.edu.in/raghava/il6pred/How to install the package, type the following commandpipinstallil6predMinimum USAGETo know about the available option for the CLI tool, type the following command:il6pred-hil6pred-ipeptide.fa``Thiswillpredicttheinterleukin-6inducingpotentialofsequenceinfastaformat.Itwilluseotherparametersbydefault.Itwillsaveoutputin"outfile.csv"inCSV(commaseparatedvariables).

**FullUsage:**Followingiscompletelistofalloptions,```bash

il6pred[-h]-iINPUT[-oOUTPUT][-j{1,2,3}][-tTHRESHOLD][-w{5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25}][-d{1,2}]optionalarguments:-h,--helpshowthishelpmessageandexit-iINPUT,--inputINPUTInput:proteinorpeptidesequenceinFASTAformatorsinglesequenceperlineinsinglelettercode-oOUTPUT,--outputOUTPUTOutput:Fileforsavingresultsbydefaultoutfile.csv-j{1,2,3},--job{1,2,3}JobType:1:predict,2:designand3:scan,bydefault1-tTHRESHOLD,--thresholdTHRESHOLDThreshold:Valuebetween0to1bydefault0.11-w{5,6,7,..,25},--winlengWindowLength:5to25(scanmodeonly),bydefault10-d{1,2},--display{1,2}Display:1:Interleukin-6inducingpeptide,2:Allpeptides,bydefaIL6PredInput File:It allow users to provide input in two format; i) FASTA format (standard) and ii) Simple Format. In case of simple format, file should have one one peptide sequence in a single line in single letter code (eg. peptide.seq). Please note in case of predict and design module (job) length of peptide should be upto 25 amino acids, if more than 25, program will take first 25 residues. In case of scan module, minimum length of protein/peptide sequence should be more than equal to window length (pattern), see peptide.fa . Please note program will ignore peptides having length less than 8 residues (e.g., protein.fa).Output File:Program will save result in CSV format, in case user do not provide output file name, it will be stored in outfile.csv.Threshold:User should provide threshold between 0 and 1, please note score is propotional to interleukin-6 inducing potential of peptide.Address for contactIn case of any query please contactProf. G. P. S. Raghava, Head Department of Computational Biology,            
Indraprastha Institute of Information Technology (IIIT), 
Okhla Phase III, New Delhi 110020 ; Phone:+91-11-26907444; 
Email: raghava@iiitd.ac.in  Web: http://webs.iiitd.edu.in/raghava/