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General FAQ
How can I order?
What is a Fasta format for a protein sequence?
I have the gene sequence, is it OK?
How do you guarantee confidentiality?
Why paying for simulations?
Protein Investigator FAQ
What is the interest of Protein Investigator as compared to using Net services on my own?
Why should I use Protein Investigator?
How are Protein Investigator results provided?
What can I expect from Protein Investigator?
What about the sequence characteristics?
What about the structural information
What about 3D structure?
What about the putative functional roles
What about my particular case
How long before I get Protein Investigator results?
What is the accuracy/reliability of the method? What do you mean by accuracy/reliability of methods?
Does Protein Investigator report include explanations for methods?
Reading the report we had a few ideas on what could be our problems, could you help us? Could you go deeper with the analysis? Can we discuss that point, how?
Epiros FAQ
What can I expect from Epiros?
How are Epiros results provided?
Which information can I expect from Epiros?
Can I use Epiros to find all antigenic sites of my sequence / Does Epiros give only the most relevant antigenic sites?
Is it possible to specify the experimental method used?
Which methods do you use for prediction?
What is the accuracy/reliability of the method?
How long before I get Epiros results?
You say that antibodies show mixed results in different types of screening assays; what does that mean?
Does Epiros report include explanations for methods?
What length are the predicted peptides?
What are the advantages of your method as compared to others?
If the question you are looking for is not available, then please send us your question at info@biosiris.com.
General FAQ
What is a Fasta format for a protein sequence?
I have the gene sequence, is it OK?
How do you guarantee confidentiality?
Why paying for simulations?
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How can I order?
You will find an order form on the Biosiris web site (www.biosiris.com). In the ‘Product & Services’ area, select ‘Service appliance’ and go to the product you are interested in.
Direct links are:
http://www.biosiris.com/Online_order/Epiros/Epiros_order.php
http://www.biosiris.com/Online_order/ProteinInvestigator/ProteinInvestigator_order.php
Complete all fields. Quotation will be send back to you by e-mail.
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What is a Fasta format for a protein sequence?
Fasta format is the standard format for protein sequences.
It is composed of a header line (beginning with a '>') which gives a name and/or a unique identifier for the sequence, and often other information too. The simple format of Fasta files makes them easy to manipulate using text processing tools and scripting languages. The sequence is written in a one-letter code.
Here is an example of sequence in Fasta format:
>SEQUENCE_1
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
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I have the gene sequence, is it OK?
Yes. The gene sequence can easily be translated into protein sequence. The latter will be used for further analysis.
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How do you guarantee confidentiality?
If your sequence is under patent and/or if you want to secure data transmission, your sequence can be sent with secured mail. Otherwise, we use regular e-mail or mail.
The report is confidential and the documents or information exchanged between the parties cannot be communicated or disclosed to third parties (see General Conditions for more details).
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Why paying for simulations?
Thanks to Biosiris expertise, bioinformatics and predicting tools will help you saving time and money!
Biosiris will help you making the good strategic choice for Research & Developments concerns. Biosiris services will help you limit the number of experimental studies. Biosiris will give you an external and expert point of view on your problem or question.
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Protein Investigator FAQ
What is the interest of Protein Investigator as compared to using Net services on my own?
Why should I use Protein Investigator?
How are Protein Investigator results provided?
What can I expect from Protein Investigator?
What about the sequence characteristics?
What about the structural information
What about 3D structure?
What about the putative functional roles
What about my particular case
How long before I get Protein Investigator results?
What is the accuracy/reliability of the method? What do you mean by accuracy/reliability of methods?
Does Protein Investigator report include explanations for methods?
Reading the report we had a few ideas on what could be our problems, could you help us? Could you go deeper with the analysis? Can we discuss that point, how?
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What is the interest of Protein Investigator as compared to using Net services on my own?
Sequence analysis software, available as Net services, are mainly addressed to experts in bio-informatics. Biosiris helps non-expert scientists: Biosiris sorts out market technologies, keeps the best and watches for changes and updates. Biosiris also selects the relevant data and gives an external expert point of view.
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Why should I use Protein Investigator?
Protein Investigator gives the maximum information about your protein in the minimum time and for low cost. It is a really good start point for researchers.
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How are Protein Investigator results provided?
All the results of the analysis, discussion and correlation of the results, ideas for deepened analysis… are included in a clear, precise and relevant report.
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What can I expect from Protein Investigator?
Protein Investigator includes sequential, structural and functional information. In order to give the more complete and comprehensive report, we correlate the whole information.
Protein Investigator report will help you to decide what to do with your protein!
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What about the sequence characteristics?
First, you will find general information like molecular weight. Then, the composition of the sequence is analyzed for particular frequencies of amino acids, amino acid families or charge ratio.
Charge clusters and repetitive motifs are detected and analyzed.
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What about the structural information ?
Several secondary structure predictors are tested and their results compared.
For each cysteine of your sequence, probable disulfide bonds are highlighted.
Transmembrane helices, coiled coils, low complexity and disordered regions are predicted. Reliability of the results is estimated and implication for the protein behavior discussed.
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What about 3D structure
If no experimental 3D structure exists, we will provide you global information about the tertiary structure of your protein (mainly alpha, mainly beta structures, membrane domains).
If a model of the 3D structure can be constructed, it will be explained at the end of the report (‘further interesting bioinformatics analysis’) and can be done in a further customized service.
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What about the putative functional roles ?
Protein Investigator will detect potential signal peptides, protein domains, functional motifs, interaction sites and antigenic sites. All these data will be correlated to predict possible functional roles of your protein.
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What about my particular case ?
If you have a particular question for your protein sequence, all the information brought together will be discussed to propose a first answer. Some supplementary analysis can be done (conservation of residues for example).
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How long before I get Protein Investigator results?
Delays for Protein Investigator are about a month. After you order, delays will be confirmed and specified.
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What is the accuracy/reliability of the method? What do you mean by accuracy/reliability of methods?
Protein Investigator uses a great number of methods and algorithms each having its own accuracy (cited in the report). For each method, the best parameters and most up to date algorithms are used. Nevertheless, it is important to keep in mind that the study is made of predictions and that it may not be considered as sure but more likely as hypothesis for your experimental studies.
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Does Protein Investigator report include explanations for methods?
Yes. For each method used, a clear and summarized explanation is done to help non-expert to understand methods. Results and reliability of the results are discussed.
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Reading the report we had a few ideas on what could be our problems, could you help us? Could you go deeper with the analysis? Can we discuss that point, how?
Yes. At the end of each Protein Investigator report, you will find a proposal for further analysis to deepen the comprehension of your protein properties. These proposals can be achieved via customized services with Biosiris (info@biosiris.com).
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Epiros FAQ
What can I expect from Epiros?
How are Epiros results provided?
Which information can I expect from Epiros?
Can I use Epiros to find all antigenic sites of my sequence / Does Epiros give only the most relevant antigenic sites?
Is it possible to specify the experimental method used?
Which methods do you use for prediction?
What is the accuracy/reliability of the method?
How long before I get Epiros results?
You say that antibodies show mixed results in different types of screening assays; what does that mean?
Does Epiros report include explanations for methods?
What length are the predicted peptides?
What are the advantages of your method as compared to others?
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What can I expect from Epiros?
Epiros gives you the mot probable antigenic sites of your protein in the minimum time and for low cost. It is a really good start point for antibody studies. It should also help you when your experimental results are not satisfactory.
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How are Epiros results provided?
All the results of the analysis, discussion and most probable epitopes are included in a clear, precise and relevant report.
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Which information can I expect from Epiros?
Epiros report includes a short explanation of variables used in the prediction method. Epiros report gives you the antigenic score of your amino acid sequence.
The distribution of the score is discussed and the best antigenic sites are proposed (depending on experimental methods used). The possibility of cross-reactivity is also discussed.
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Can I use Epiros to find all antigenic sites of my sequence / Does Epiros give only the most relevant antigenic sites?
Epiros antigenic score enables the detection of all probable antigenic sites of your sequence. Moreover, the report includes a selection of best antigenic sites. These correspond to optimized antigenic peptides.
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Is it possible to specify the experimental method used?
Yes. When you complete the order form, you can indicate experimental method used (Elisa, Western Blot, Immuno-Precipitation, Staining of tissues or other methods).
Selection of the best antigenic peptides is done depending on your experimental study.
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Which methods do you use for prediction?
We use a wide range of methods. Some are free published methods and others are proprietary methods (developed from biological databases).
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What is the accuracy/reliability of the method?
With Epiros, the accuracy of linear B-epitopes prediction is increased up to 80%. Classical free methods have an accuracy of about 65%.
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How long before I get Epiros results?
Delays for Epiros are about two weeks. After you order, delays will be confirmed and specified.
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You say that antibodies show mixed results in different types of screening assays; what does that mean?
Depending on your experimental conditions, you will detect different types of epitopes: some methods will totally or partially alter protein structure; other methods will make some amino acids inaccessible… All these parameters will be taken into account when we predict the best antigenic sites.
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Does Epiros report include explanations for methods?
Yes. For each variable used, a clear explanation is done. The epitope score calculations are explained and score interpretation is discussed. We also briefly describe methods used to select the most probable antigenic residues.
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What length are the predicted peptides?
The length of predicted peptides will be chosen for maximal reactivity. The optimal length will depend on the protein sequence and protein domains. Generally, the length varies between 10 and 18 amino acids and will be optimized to reduce experimental costs (minimal size).
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What are the advantages of your method as compared to others?
Epiros will combine free and simple methods with proprietary technologies. Epiros will give you the optimal antigenic sites for a minimal cost.
The major justification to use Epiros is the possibility to select epitopes fitting best to your experimental conditions.
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