Generating genomic platforms to study Candida albicans pathogenesis

Mélanie Legrand; Sophie Bachellier-Bassi; Keunsook K. Lee; Yogesh Chaudhari; Hélène Tournu; Laurence Arbogast; Hélène Boyer; Murielle Chauvel; Vitor Cabral; Corinne Maufrais; Audrey Nesseir; Irena Maslanka; Emmanuelle Permal; Tristan Rossignol; Louise A. Walker; Ute Zeidler; Sadri Znaidi; Floris Schoeters; Charlotte Majgier; Renaud A. Julien; Laurence Ma; Magali Tichit; Christiane Bouchier; Patrick Van Dijck; Carol A. Munro; Christophe d’Enfert

CandidaOrfDB was created to integrate the data of the C. albicans ORFeome project and is available at http://candidaorfeome.eu. The database is a relational database using the SQL database server Oracle with a web interface developed using J2EE. The alignment algorithm uses biojava3-alignment Java library, implemented with a NeedlemanWunsch aligner, configured with a gap open penalty of 5 and a gap extension penalty of 2. The substitution matrix used is named "nuc-4_4" and was created by Todd Lowe (https://github.com/sbliven/biojava/blob/master/biojava3-alignment/src/main/resources/nuc-4_4.txt). The alignment algorithm was specifically customized for CandidaOrfDB to work on segments of 500 codons, which provides an optimized alignment performance for C. albicans average sequence length. author/funder. All rights reserved. No reuse allowed without permission.