Similar protocols

Pipeline publication

[…] dentified Arabidopsis TIFY sequences were first submitted to the Pfam database (http://pfam.sanger.ac.uk) to obtain the domain architecture of this family. The TIFY domain, Jas and CCT motifs were found to be represented by Pfam accession numbers PF06200, PF09425 and PF06203, respectively. Searches for each domain within the Grape Genome Database (12X; http://www.genoscope.cns.fr) were performed using HMMER with an E-value <1e-6. To confirm results obtained using the HMMER algorithm, protein motifs were also queried against the Pfam database., Multiple alignments of ZML, PPD, and JAZ protein sequences from Vitis vinifera, Arabidopsis thaliana and Oryza sativa were performed using the ClustalW program . Phylogenetic trees were constructed with the MEGA 4.0 software using the maximum parsimony (MP) method and a bootstrap test that was replicated 1000 times ., The exon/intron structures of the grape ZML, PPD and JAZ genes were determined from alignments of their coding sequences with corresponding genomic sequences using the est2genome program, which aligns spliced mRNA sequences to the genome to obtain the exon/intron structure of genes . A diagram of exon/intron structures was obtained using the online Gene Structure Display Server (GSDS: http://gsds.cbi.pku.edu.cn), which exhibited both exon position and gene length. Since the introns of several of the genes analyzed were relatively long, only the coding exons were drawn to scale., Tandem duplications of ZML, PPD and JAZ genes in the grape genome were predicted by determining their physical locations on individual chromosomes. Tandemly duplicated genes were defined as adjacent homologous genes on a single chromosome, with no more than one intervening gene. For synteny analysis, syntenic blocks within the grape genome, as well as between grape and Arabidopsis genomes, were downloaded from the Plant Genome Duplication Database and those co […]

Pipeline specifications

Software tools Clustal W, MEGA, GSDS
Databases PGDD