In most interaction databases, duplications are prevented by checking each new entry's third-party database identifiers, such as UniProt [ 26] accessions for proteins, ENSEMBL [ 27] identifiers for genes and unique chemical identifiers such as the IUPAC International Chemical Identifier [ 28] or Chemical Entities of Biological Interest [ 29].
Thus, this initial database of duplications and deletions will be a useful research tool for investigations of the evolution of the Gossypium genome.
A search for duplicated genes using the Plant Genome Duplication Database (PGDD; http://chibba.agtec.uga.edu/duplication/) revealed the existence of three gene pairs (PtHsp90-1a/PtHsp90-1b, PtHsp90-5a/PtHsp90-5b and PtrichocarpatHsp90-5b) in P. trichocAdditionaltional file 10A) and two pairs (OsHsp90-2/OsHsp90-3 and OsHsp90-5a/OsHsp90-5b) in O. sativa (Additional file 10B).
We then searched for duplicated genomic fragments using the Plant Genome Duplication Database (http://chibba.agtec.uga.edu/duplication) and found some genes in the qRgls2 interval that share high synteny with rice genes located on chromosome 2.
The plant genome duplication database (PGDD; available at http://chibba.agtec.uga.edu/duplication/) is a public database to identify and catalogue plant genes in terms of intra-genome or cross-genome syntenic relationships.
The duplicated genes were found from the RGAP segmental duplication database http://rice.plantbiology.msu.edu/segmental_dup/100kb/segdup_100kb.shtml.shtml
To determine if other genes in the SULT super family were also recently duplicated during LCR expansions, we searched the Segmental Duplication Database [ 4] for human reference genes located on LCRs.
There are several patients also present in the DECIPHER database who have duplications overlapping this large duplication in the child, including 280 551, with hirsuitism, feeding difficulties and global developmental delay; 283 584, with sacral dimple and low set ears; 1561, with frontal bossing and sacral dimple.
NCBI databases: CAZY website: SignalP program: NetNGlyc: NCBI map viewer: PHYLIP: TIGR rice segmental duplication database: RepeatMasker: Genedoc: WT performed rice plant cultivation, RT-PCR analysis, cDNA cloning and sequencing, and drafted the manuscript.
Analysis of the TIGR rice segmental duplication database revealed 30 MADS-box genes within the duplicated segments of rice chromosomes.
