Wellcome to ISEApeaks home page
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Why ISEApeaks? |
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ISEApeaks functions |
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More information |
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Contacts |
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Why ISEApeaks ? |  |
DNA automatic sequencers are now widely used in all sorts of biological analysis to separate DNA fragments. The major ones are microsatellite analysis, Restriction or Amplified Fragment Length Polymorphism (AFLP or RFLP), Single Strand Conformation Polymorphism (SSCP), gene expression quantifications and also immune repertoire analysis by the determination of the Complementary Determining Region 3 (CDR3) size usage (1). Several softwares (GeneScan, Immunoscope...) ensure raw data generation using sequencing gels by calculating the nucleotidic size and area of bands. However no tool has been devised to enable retrieval and efficient managing of large amounts of data acquired by high throughput sequencers, thus impairing the development of particulars applications. For instance, while it is now possible to analyse immune repertoires in dozens of samples, immune repertoire data is analysed by eye on display printouts. This approach implies the existence of bias in analysis and loss of relevant information and, moreover, the amount of data makes it now impossible.
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ISEApeaks functions |
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ISEApeaks® (2) package has been designed to solve these problems. ISEApeaks is copyright of Institut Pasteur, 2000-2001. A User's Guide explains thoroughly the use of all the functionnalities of ISEApeaks.
Extraction and management of data (2)
ISEApeaks package automatically extracts the acquisition data stored in scattered files. Then, data of different samples and individuals can be gathred into a peak data base after user validation. This data base can then be used for analysis.
Analysis of lymphocyte repertoires by CDR3 length spectratypes
(Collette et al, Manuscript in preparation)
ISEApeaks takes advantage of the formed peak database to analyse objectively complex data obtained for lymphocyte repertoires. First of all, ISEApeaks performs length correction (smoothing module): in the periphery, CDR3 peaks should be spaced by three nucleotides due to selection of in-frame rearrangements. Then, ISEApeaks enables the statistical analysis of this peak database by computing perturbation and/or expansion indexes for immune repertoires. The analysis module enables the automatic analysis of large cohorts of individuals with published tests as well as scores we devised. Finally, ISEApeaks provides tools for Immunoscope data: easy creation of Immunoscope macro and of large CDR3 profile displays. This software will contribute to the high throughput analysis of immune repertoires.
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More information |
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Contacts |
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To obtain further information or to obtain ISEApeaks package, please contact one of the following persons:
Alexis COLLETTE collette@pasteur.fr
Adrien SIX
askc@pasteur.fr
Immunochimie Analytique
Patrick CORNILLE pcornill@pasteur.fr
Service de Transfert de Technologies
Institut Pasteur 25, rue du Dr Roux
75015 PARIS FRANCE
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For any suggestion or problem about this page send an e-mail to collette@pasteur.fr.