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The Protein Identifier Cross-Reference (PICR) service: reconciling protein identifiers across multiple source databases

Richard G Cote, Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler, Henning Hermjakob
2007 BMC Bioinformatics  
Conclusion: We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases.  ...  Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases.  ...  Acknowledgements PICR contributors are supported through the BBSRC ISPIDER grant and EU FP6 "Felics" (contract number 021902 (RII3)) grants. RC would like to thank KC for invaluable contributions.  ... 
doi:10.1186/1471-2105-8-401 pmid:17945017 pmcid:PMC2151082 fatcat:vegtt57cdbaslkka4ekupxyamu

Interfacing sequences and structures of proteins: applications to protein annotation and sequence feature visualization

Fabrice Pierre André David, Ron David Appel, Amos Marc Bairoch, O. Michielin
Remerciements Je tiens à remercier tout d'abord chaleureusement mes superviseurs Dr Yum  ...  The foundation of such system is a unique, bidirectional and up-to-date mapping between sequences and structures.  ...  Searching PDB reconstructed sequences similar to each UniProtKB sequence The aim of this step is to get all the matches between non-redundant PDB reconstructed sequences and non-redundant UniProtKB sequences  ... 
doi:10.13097/archive-ouverte/unige:23831 fatcat:bhzt53h5h5e2nlpa366p7nev3q

Information and Simulation Systems for the Analysis of Gene Regulation and Metabolic Pathways (Dagstuhl Seminar 01261)

Ralf Hofestädt, John Reinitz, Nikolay Kolchanov
The 2001 meeting is a sequel to the 1995 and 1998 meeting on the similar topic.  ...  The third Dagstuhl Seminar for Information and Simulation Systems for the Analysis of Gene Regulation and Metabolic Pathways was held from June, 24 to 29, 2001.  ...  The SWISS-PROT group at the EBI combines manual annotation and sequence analysis of SWISS-PROT entries with rule-based automatic annotation of TrEMBL entries to provide a comprehensive, reliable and up-to-date  ... 
doi:10.4230/dagsemrep.313 fatcat:imloyisgenaaxmkqav42bd77xy

Development of methods for the automated annotation of prokaryotic proteomes

Alexandre Gattiker, Amos Marc Bairoch, Ron David Appel
Annotation may also be supplied by as Third-Party Annotation (TPA) linked to a published paper, when such a paper refers to an already existing sequence.  ...  This clustering provides a complete coverage of sequence space while hiding redundant sequences. The non- redundancy allows faster sequence similarity searches. ...]  ...  Implementing the non-redundancy specification required the development of a program, due to the amount of data to be compared and the complexity of the comparison.  ... 
doi:10.13097/archive-ouverte/unige:726 fatcat:md3t7oqxmncxbg7zzsfbobuvpq

A genomic study of morphinan biosynthesis in the "opium poppy" Papaver somniferum L [article]

Anthony G. Millgate, University, The Australian National, University, The Australian National
Several other clones had sequence homology, however these were to sequences of unknown function. QRT-PCR analysis was used to further authenticate the non-redundant set of 10 genes/alleles.  ...  The non-spliced transcript may also translate to a protein with altered function.  ...  Sequences were analysed on BioManager by ANGIS ( against the NCBI database (GenBank main, SwissProt and SpTr EMBL databases). 2D protein Analysis.  ... 
doi:10.25911/5d65120a9e387 fatcat:sqbj5jjpezbanpbwihlaux2xku