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The primers utilized are shown in Fig. 1 Primer pairs were designed using the Primer Quest tool found on the Integrated DNA Technologies-ITD website, (http://www.idtdna.com/site).
Their primer pairs were designed using the 'Primer Quest' tool (Integrated DNA Technologies, Coralville, IA, USA) from sequences obtained in the data base (Additional file 1: Table S1).
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We also used the IMGT/HighV-QUEST tool (Giudicelli et al., 2011) to analyze our reference set, and obtained an average of 41.65% sensitivity and 96.15% precision (Table 3).
Sequences were analyzed using the IMGT databases and the IMGT/V-QUEST tool (version 3.2.17, Université Montpellier 2, CNRS, LIGM, Montpellier, France).
The scFv sequences were analysed at the nucleotide level with IMGT/V-QUEST tool (http://www.imgt.org) to identify the closer human germline genes [ 46– 46].
Sequences of the scFvs isolated after panning were compared with human germline sequences, using the IMGT/V-QUEST tool, available on-line from the International ImmunoGeneTics information system® (IMGT) (http://www.imgt.org).org
Sequencing data was processed using sequence quality and signal filters in the 454 Roche analysis pipeline, followed by identification of conserved framework regions and V germline gene identification using the IMGT/HighV-Quest Tool.
The scFvs in bold were of particular interest for this study After the isolation and the sequencing of the scFvs, a computational analysis using IMGT/V-QUEST tool was performed to retrieve the human germline sequences closer to the sequence of the 24 selected scFvs.
Finally, in order to classify the sheep TRAV pseudogenes with frameshifts (which were not included in the tree), we analysed their V region sequences with the IMGT/V-QUEST tool [ 23, 24] using the option 'Search for insertions and deletions in V-REGION' and aligned with the germline human TRAV sequence set from the IMGT reference directory.
The genetic origin of sequences encoding the heavy and light chain variable (VL) domains, and mutational status of the transcripts was determined using the IMGT/V-QUEST web tool (program version 3.2.20; reference directory release: 201135-3) 25.
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