BTXpred Server Help Page

General Information

A toxin (Latin toxicum, poison) is a specific substrate, often a metabolic product of the organism that damages the host. Bacterial toxins, which are synthesized inside bacterial cells, are classified according to how they are releases. Exotoxins are soluble substance secreted into host tissues. Endotoxins are incorporated into cell wall and released into host tissues, when bacteria die.Endotoxins are mainly LPS (Gram negative bacteria) or in some special cases, a toxin tightly associated with the cell wall (some Gram positive bacteria are thought to have non-LPS endotoxin-like molecules).
We collected annotated bacterial toxins from SWISS-PROT and developed Support Vector Machine (SVM) based method that can discriminate bacterial toxins from non-toxins with accuracy of 96.07% using five fold cross validation. We developed a method that can classify exotoxins and endotoxins with accuracy of 95.71%.
Further, we have classified exotoxins proteins into seven different functions depending upon their molecular targets i) activate adenylate cyclase, ii) activate guanylate cyclase, iii) food poisioning iv) neurotoxins, v) macrophage cytotoxin, vi) vacuolating cytotoxin and vii) thiol activated and made profile database of the seven different functions using Hidden Markov Model (HMM). We used leave one out cross validation of seven different functional exotoxins and achieved an overall accuracy of 95.75% using HMM, where as PSI-Blast achieved an overall accuracy of 97.87%.

Stepwise HELP

1.Name of Protein:- This is an optional field. It can have any alphabet and numbers with "-" or "_".

2.Protein Sequence:-BTXpred server allows the submission of sequence in any of the standard formats. The users can paste primary sequences in the provided inbox. The server also has the facility for uploading the local sequence files.

3. Sequence format:- The server can accept both the formated or without formatted primary protein sequences. The users should choose weather the sequence uploaded or pasted in plain or formated before running prediction.

4. Selection of types of predictions:- The server allows 3 types of prediction, select them

Bacterial toxin or non-toxin (You can choose SVM and PSI-BLAST; but not HMM)

Types of Toxin- endo toxin or exotoxin(You can choose SVM and PSI-BLAST; but not HMM)

Function of exotoxins( you can choose PSI-BLAST and HMM; but not SVM)

5. Prediction Approach:- The server allows the prediction on the basis of three different approaches, Select any one out of them

• SVM (For Toxin and types of toxin)
• PSI-Blast (For Toxin, Types of Toxin, and functions of exotoxins)
• HMM (Only for function of exotoxins)