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InPrePPI Biological Background
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Answers:
What is InPrePPI? Why I should use it?
InPrePPI was developed at the Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences to investigate the functional linkages between proteins with non-homology-based methods. InPrePPI is the abbreviation of "an Integration method for Prediction of Protein-Protein Interactions", which integrated Phylogenetic profiles method, Gene neighbors method, Gene fusions method, and Gene clusters (operon) method to infer the protein-protein interactions or gene functional linkages.
By InPrePPI, you can predict the function linkage of two genes, annotate the unknown gene/genome with these linked genes, produce a great deal of networks for properties analysis, and so on.
How can I cite the InPrePPI?
Please cite: Sun, J., Sun Y., Ding G., et al. "InPrePPI: an integrated method based on genomic context to predict protein-protein interactions. (Submitted)"
Can everybody use InPrePPI? Can I use InPrePPI for commercial purposes?
InPrePPI is free of charge for academic and non-profit use. The source code is released under the GNU General Public License (GPL). If you want to use it for commercial purposes, please contact
yxli@sibs.ac.cn
first.
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InPrePPI Biological Background
Why can InPrePPI predict the protein-protein interaction?
All the four methods implemented in the InPrePPI infer functional linkages between proteins by identifying pairs of non-homologous proteins that co-evolved. Evolutionary pressure dictates that pairs of proteins that function in concert are often both present or absent within genomes (Phylogenetic profiles method), tend to be coded nearby in multiple genomes (Gene neighbors method), might be fused into a single protein in some organisms (Gene fusions method) or are components of an operon (Gene clusters method). In contrast, if proteins are not related by function, they need not appear together or exhibit spatial proximity in the genome (Genome Biology 2004, 5:R35). That is the basic hypothesis of InPrePPI.
What are "PPM", "GFM", "GNM" and "GCM"?
"PPM" stands for "Phylogenetic profiles method", "GFM" for "Gene fusions method", "GNM" for "Gene neighbors method", "GCM" for "Gene clusters (operon) method". We have listed the references related to these methods in
http://www.biosino.org/InPrePPI/articles.jsp. Detailed information can be obtained from this web page.
For more details about SHOPS, see
Bioinformatics. 2004 Nov 1;20(16):2644-55
and
http://www.bioinformatics.med.uu.nl/shops/
.
Are the reference genomes enough to reflect the evolution background of the genes?
We have discussed this problem in aother two papers:
Sun, J., J. Xu, et al. (2005). "Refined phylogenetic profiles method for predicting protein-protein interactions." Bioinformatics 21(16): 3409-15.
Sun,J.,Li,Y., et al. "Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms? (Submitted)
Can I choose special organisms as reference genomes in the InPrePPI website?
Yes, you can. That is a distinctive feature of the InPrePPI website. All the organisms in the current InPrePPI's reference genomes dataset are listed in the text box and can be multi-selected.
Can I build my own reference genomes dataset in house?
Yes, you can do it locally. You must install InPrePPI locally and run on your computer.
Can I choose all the five methods to do the protein-protein interaction at the same time?
You can not run all the five methods once. You can choose the four methods including Phylogenetic profiles, Gene fusions, Gene clusters and Gene neighbors methods, or the InPrePPI methods solely.
What is the "job id"?
The "job id" or "InPrePPI-DATE-UNIQUEID" is a unique id of the job you submitted. You can retrieve the result of a job using the job id for 3 days.
What is the Id2gi-description file?
The Id2gi-description file is a mapping file between IDs and protein descriptions extracted from original the FASTA file. The IDs are used to denote the nodes in the graphic presentation of the protein-protein interactions by bioverse.
Why can not I see the graphic interactions?
The graphic presentation is implemented by bioverse and requires the support of java applet. Please download the SUN JVM to support applet. Still failed? Please check configuration of your browser. We tested it well on IE6.0 and Mozilla Firefox.
How long will be my result gotten?
It is based on your size of the job. A genome with three thousand genes will be finished in eight hours. The server now accepts the sequence set with less than 1000 genes. If you have huge genome/sequence set, local installation is recommended.
Why can't I get the result after I submit the sequence?
Be patient if you submit the sequences just now and your data set is not large than 1000 sequences. Otherwise, let us know, please email to ysun@sibs.ac.cn.
Why some method can't be executed?
Each method has some required input files/parameters which are marked with red star symbol (*) in the web page. If you did not set these required elements of the method, it would be canceled.
What is the purpose of "select few organisms"?
It takes a long time to execute the jobs if you select more than 100 reference organisms. We provide 261 organisms selected as default, but if you want to do a quickly view of our application, it's recommended to select 10 reference organisms for test.
What the row headings are in the result files?
The row heading in the result files of
Phylogenetic profiles method, Gene
neighbors method, Gene fusions method,
and Gene clusters (operon) method is
"Protein 1<tab>Protein
2<tab>Analysis method<tab>Score",
while the row heading of the InPrePPI
method is "Protein
1<tab>Protein
2<tab>Analysis method<tab>[scores in
each method(profiles method, Gene
neighbors method, Gene fusions method,
and Gene clusters (operon) method)]<tab>InPrePPI score.
How do I install/uninstall InPrePPI locally? What is the basic system requirement?
Download the source file from
http://inpreppi.biosino.org/InPrePPI/download.jsp
, uncompress the compressed package. A README file in the compressed package will give you more information on installing the InPrePPI locally and the system requirement.
If you want to uninstall the InPrePPI, delete it from your disk. It is a green software.
Can I download the source code for InPrePPI applications? Is a license required?
OK, no problem. It is free and released under the
GNU General Public License (GPL)
.
What computer language is needed to understand the source code of InPrePPI application?
Java, C++.
Can I use the InPrePPI method in other fields of biology?
Yes, you can.
Why was the Phylogenetic profile method written in C++ language but not Java?
The PPM is rewritten in C++ for speed consideration.
How to report a bug?
Email to
ysun@sibs.ac.cn
.
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