Welcome to Galaxy based service in OSDDlinux Online


Galaxy is a open source web-based platform which can meet the needs of bioinformaticians analysing the bulk data. Users can use galaxy without command line since it is a graphical user interface. We have integrated GPSR1.0, GPSR2.0 along with the webservers and the standalone in the OSDDlinux which can help the users and the scientists in drug discovery.

- Users can make workflows, manipulate workflows and use the pre-existing workflows for the pipeline used in the drug discovery.

- Heavy jobs are automatically saved in the history panel which can can be accessed later on.

- Available at: LiveGalaxy

Following is the list of the available LiveGalaxy packages integrated in the OSDDlinux.

GPSR1.0

ProgramDecription
fasta2sfastaConvert fasta format to single fasta format
pro2aacTo calculate amino acid composition of protein
pro2aac_ntTo calculate amino acid composition of N-terminal (nt) residues of a protein
pro2aac_ctTo calculate amino acid composition of C-terminal (ct) residues of a protein
pro2aac_rest.plTo calculate amino acid composition of a protein after removing N-, and C-terminal residues
pro2aac_splitTo calculate split amino acid composition (SSAC) of a protein
pro2dpcTo calculate dipeptide composition of protein
pro2dpc_ntTo calculate dipeptide composition of N-terminal (nt) residues of a protein
pro2dpc_ctTo calculate dipeptide composition of C-terminal (ct) residues of a protein
pro2tpcTo calculate tripeptide composition of protein
add_colsTo add columns of two files
col2svmTo generating SVM_light input format
col_multTo multiplying each column of input file with a number
col_mult_selTo multiplying selective columns with a number
col_remTo remove selective columns from a file
col_extTo extract selective columns from a file
col_corrTo compute correlation co-efficient between two column
col_avgTo calculate average column of two files
seq2pssm_impTo calculate PSSM matrix in column format without any normalization
pssm_n1To normalize pssm profile based on 1/(1+e-x) formula
pssm_n2To normalize pssm profile based on (numb -min)/(max -min) formula
pssm_n3To normalize pssm profile based on (numb -min)*100/(max -min) formula
pssm_n4To normalize pssm profile based on 1/(1+e-(x/100) formula
pssm_compTo compute PSSM composition (400 points)
col_sigSignificance of columns in two column files
pssm2patTo generate patterns of given size from PSSM matrix
pssm_smoothTo designed smooth pssm profile for plot
seq2motifTo create motifs by sliding window of user defined length with option of adding terminal X
motif2binTo make binary input from the multifasta motif file
blast_similarityTo perform blast

GPSR2.0

Tools for Chemo-informatics: Part A

ProgramDiscription
desc_imp_aGives n most important descriptors for predicting positive and negative examples (n given by user)
desc_sel_aSelects the final set of descriptors for prediction by removing very similar descriptors
desc_graph_aCreates barplot of importance of descriptors (in terms of IDD) vs important Descriptors
desc_mod_aModifies the binary descriptors based on relative frequency in positive and negative datasets
desc_clust_aPerforms clustering of descriptors (i.e. column wise) with graphical representation
chem_clust_aPerforms clustering of chemicals (i.e. row wise) with graphical representation
sim_chem_aFinds the most similar chemical from the database of chemicals based on distance between descriptors of chemicals

Tools for Chemo-informatics: Part B

ProgramDiscription
desc_imp_bGives n most important descriptors for predicting positive and negative examples (n given by user)
desc_sel_bSelects the final set of descriptors for prediction by removing very similar descriptors
desc_graph_bCreates barplot of importance of descriptors (in terms of IDD) vs important Descriptors
desc_clust_bPerforms clustering of descriptors (i.e. column wise) with graphical representation
chem_clust_bPerforms clustering of chemicals (i.e. row wise) with graphical representation
sim_chem_bFinds the most similar chemical from the database of chemicals based on distance between descriptors of chemicals

Tools for Chemo-informatics: Part C

ProgramDiscription
desc_imp_cGives n most important descriptors for predicting positive and negative examples (n given by user)
desc_sel_cSelects the final set of descriptors for prediction by removing very similar descriptors
desc_graph_cCreates barplot of importance of descriptors (in terms of IDD) vs important Descriptors
desc_clust_cPerforms clustering of descriptors (i.e. column wise) with graphical representation
chem_clust_cPerforms clustering of chemicals (i.e. row wise) with graphical representation

Tools for Chemo-informatics: Part D

ProgramDiscription
desc_imp_dGives n most important descriptors based upon correlation with response. (n given by user). An additional file with all descriptors with correlation values is also given as output
desc_sel_dSelects the final set of descriptors for prediction by removing very similar descriptors
desc_graph_dCreates barplot of importance of descriptors (in terms of IDD) vs important Descriptors
desc_clust_dPerforms clustering of descriptors (i.e. column wise) with graphical representation
chem_clust_dPerforms clustering of chemicals (i.e. row wise) with graphical representation

Miscellaneous

ProgramDiscription
make_selectedfileExtracts specific columns from input file and writes in output file
shiftcolShifts the 2 columns in a file and writes in an output file
rem_identicalcolRemoves identical columns in a file and writes unique columns in output file
matrix_optimizationFor a given positive and negative dataset of protein sequences this program optimizes the substitution matrix which can be used in classification of positive and negative examples
randomizefileshuffles the rows of a file randomly and writes in an output file. (can also extract user defined number of lines randomly from input file and write in output file)
meanCalculates row wise or column wise mean of file in csv format
medianCalculates row wise or column wise median of file in csv format
stdevCalculates row wise or column wise standard deviation of file in csv format
stderrCalculates row wise or column wise standard error of file in csv format
correlationCalculates correlation of all columns of a file or between 2 columns
barplotDraws a barplot between 2 properties
rocDraws a roc plot.
PSSM-patternMakes PSSM profile of positive and negative patterns for prediction at residue level (see gpsr_1.0 manual for residue level prediction)

Protein Structure

ProgramDiscription
PepStr 3D structure prediction of bioactive peptides
AlphaPred Prediction of Alpha turns in protein
APSSP2 Advanced Protein Secondary Structure Prediction Server
AR_NHPred Prediction of aromatic backbone NH interaction in proteins
TBBPred Prediction of Transmembrane Beta Barrel in Proteins
BetatPred Prediction of betaturns in proteins
BetatPred2 Prediction of betaturns in proteins
BetaTurnsPrediction of betaturn types in protein
BhairPred Prediction of Beta Hairpins
CHpredict Prediction of CH..O and CH..Pi interactions
Gammapred Prediction of Gamma turns in protein
SARpred A neural network based method predicts the real value of surface acessibility (SA) by using multiple sequence alignment

Protein Function

ProgramDiscription
NRpredA server for classification of nuclear receptors
ESLpredSVM Based Method for Subcellular Localization of Eukaryotic Proteins
PSLpredPrediction of subcellular localization of bacterial proteins
BTXpred Prediction of Bacterial Toxins
GPCRsclassClassification of amine type of G-protein-coupled receptors
SRTpredSVM-based method for the classification of protein sequence as secretory or non-secretory protein
HSLpredA server for the prediction of the subcellular localization of human protein
GSTpredPrediciton of Glutathione S-transferase protein
GlycoppA webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s)
GlycoepIn silico platform for prediction of N-, O- and C-Glycosites in eukaryotic protein sequences
NTXpredPrediction of Neurotoxins and its source and probable function from primary amino acid sequence
VICMpredPrediction of Virulence factors, Information molecule, Cellular process and Metabolism molecule in the Bacterial proteins
ALGpredPrediction of allergenic proteins and mapping of IgE epitopes
PseaPredPrediction of proteins secreted by malarial parasite P.falciparum into infected-erythrocyte
RSL-PredA SVM based method for subcellular localization prediction of rice proteins
IssPredIntein Splice Site Prediction
TBPredSupport Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs
PROprintPrediction of physical or functional interactions between protein molecules
Hivcopred Server for prediction of HIV coreceptor usage

Molecular Interaction

ProgramDiscription
ATPintPrediction of ATP interacting protein residues
GTPbinder Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information
NADbinder Prediction of NAD interacting residues in proteins
FADpred A webserver for the prediction of FAD interacting residues
Pprint A tool for predicting RNA-binding residues of a protein
PreMieR A webserver for the prediction of Mannose Interacting residue
VitaPred Prediction method for the vitamin-interacting residues in protein sequences
PROprintPrediction of physical or functional interactions between protein molecules
nHLAPred A neural network based MHC Class-I Binding Peptide Prediction Server

Therapeutic peptides

ProgramDiscription
CellPPD CellPPD predicts the cell penetration efficiency of the peptides
TumorHPDTumorHPD predicts the tumor homing property of the peptides
AntiBP A server for the prediction of the antibacterial peptides
AntiBP2 A server for the prediction of the antibacterial peptides

Subcellular localization

ProgramDiscription
ESLpredSVM Based Method for Subcellular Localization of Eukaryotic Proteins
ESLpred2ESLpred2 is an improved version of ESLpred, for predicting eukaryotic sub cellular localization
RSLpredA SVM based method for subcellular localization prediction of rice proteins
PSLpredPrediction of subcellular localization of bacterial proteins
HSLpredA server for the prediction of the subcellular localization of human protein

Annotation of Nucleotide Sequences

ProgramDiscription
DesirmDesigning of Highly Effective Complementary and Mismatch siRNAs for Silencing a Gene
EGpred Eukaryotic Gene prediction finder
SRF Spectural Repeat finder
PolApred Prediction of polyadenylation signal
Marspred Prediction of mitochondrial aminoacyl-tRNA synthetases
IcaarsIdentification & classification of aminoacyl-tRNA synthetases

Vaccine Design

ProgramDiscription
CTLpred Prediction of cytotoxic T cell epitopes
ABCpredPrediction of B-cell epitopes in antigen sequence
BCEpredPrediction of linear B-cell epitopes, using physico-chemical properties
LBtopePrediction of linear B-cell epitopes
CHEMOpredA server to predict chemokines and their receptors
CBtopeConformational B-cell epitope prediction
PropredPrediction of HLA-DR binding sites
Propred1Prediction of promiscuous MHC Class-I binding sites
PCleavagePrediction method for proteasome cleavage
TAPpredPredicting binding affinity of peptides toward the TAP transporter
HLADR4predSVM and ANN based HLA-DRB1*0401(MHC class II alleles) binding peptides prediction

Drug Design

ProgramDiscription
KiDoQDesigning of inhibitors against Dihydrodipicolinate synthase (DHDPS)
ToxinpredDesigining and prediction of toxic peptides
DrugMintA method developed for predicting drug-likelihood of a compound
MetapredPrediction of Cytochrome P450 isoform responsible for metabolizing a drug molecule
GDoQPrediction of GLMU inhibitors using QSAR and AutoDock