Computational protocol: Transcriptional activity of transposable elements in maize

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Protocol publication

[…] Model TE sequences were obtained from the TIGR Plant Repeat Databases [], Retrotransposon Database [] and GeneBank. Only well characterized elements were included in our analysis (Table ). Model sequences were compared with the maize (Zea mays L.) entries in NCBI dbEST release 092509 [], which contained 2,018,634 sequences from 315 cDNA libraries, using BLASTN analysis []. BLAST analysis were performed using an expected threshold of 10, a word size of 11, a match/mismatch of 2-3 and gap cost existence of 5 and extension of 2. We only considered positive such sequences showing an e-value < 1E-20. For organ-specific expression analysis libraries in the UniGene data set constructed from the same (or related) organ(s) were assigned into common pools. Libraries with insufficient information regarding the source organ or constructed from mixed parts of the plant were excluded from the analysis. These efforts resulted in organ groupings each containing different numbers of libraries and ESTs (Table ). The differences in the clone numbers between organ groups do not allow a direct comparison of EST numbers. A normalization process was done dividing the number of ESTs by the total number of sequences in the organ group. Normalization values were expressed as 1 per 10.000.Sequence alignments were performed using CLUSTALW and phylogenetic trees using neighbour joining method. Graphic representation of phylogenetic trees were prepared using Dendroscope v.2.7.4 []. […]

Pipeline specifications

Software tools BLASTN, Clustal W, Dendroscope
Databases TIGR Plant Repeat Databases dbEST
Application Phylogenetics
Organisms Zea mays, Mus musculus, Homo sapiens