Usually, upon retrieval, it is beneficial to supplement such identifier with retrieval date, resource version (if given) and a checksum as a tool for ultimate integrity control.
Therefore, to gain insights into the structural and functional attributes of NCX family of proteins in plants, in the present study, we have carried out whole genome analyses to identify NCX domain containing proteins in Arabidopsis and rice genomes using TAIR (The Arabidopsis Information Resource) version 10 and RGAP (Rice Genome Annotation Project) release 7, respectively.
We used the PhosphoBase resource (version 2.0) (now called Phospho.Elm: http://phospho.elm.eu.org) as a source of diverse peptide substrates for kinases [19].
GO analysis was performed using the DAVID bioinformatics resource version 6.7 (Huang et al., 2009a, 2009b).
We therefore compared predicted transcripts with 39 361 TheR9 (The Arabidopsis Information Resource version 9) gene models (http://www.arabidopsis.org).org
A second true positive dataset based on the annotation from the Domino (Ceol et al., 2007) resource (version 2009-10) walsolso assembled.
The Monarch butterfly Danaus plexippus genome resource (version 2) was obtained from MonarchBase (Zhan and Reppert 2013) through the web site at http://monarchbase.umassmed.edu/resource.html (last accessed June 10 , 2014.
The specifically/preferentially expressed genes of rice and Arabidopsis stigmas were acquired directly from published data [ 12, 13], and their annotations were updated by using Rice Genome Annotation Project release 7 [ 66] and Arabidopsis Information Resource version 10 [ 41].
The complete genome, proteome sequences and GFF (General Feature Format) of Arabidopsis and pear downloaded from The Arabidopsis Information Resource (version 10; http://www.arabidopsis.org) and http://peargenome.njau.edu.cn, respectively.
In brief, primary proteins of G. max version 1.1 were compared to the UniRef100 protein database (version 11/26/2012, [ 20] and all predicted proteins from the A. thaliana genome (The Arabidopsis Information Resource version 10) using BLASTP (E<10-6, BLAST version 2.2.27, [ 52].
