Computational protocol: Putrescine independent wound response phenotype is produced by ODC-like RNAi in planarians

Similar protocols

Protocol publication

[…] Short sequences of DjODC1, DjODC2 were retrieved from a DGE library containing differentially expressed TAGs obtained by comparison of a wild-type D. japonica DGE library and a 5 Gy-treated animal DGE library during the repopulation process that occurs after low-dose X-ray treatment (unpublished data). For the analysis, each transcript was compared to nucleotide databases (“nucleotide collection” database and “expressed sequence tags” database) by one-against-all alignments on BLAST (blastn function). DjODC1, DjODC2 sequences met at least one perfect-matching transcript, and this allowed us the expand their nucleotide sequences. In addition, imperfect matches led us to find other nucleotide sequences, similar but not identical to those of DjODC1 and DjODC2. These transcripts, were named DjODC3, DjODC4, DjODC5 and DjODC6, and their sequences are significantly different from each other, at both nucleotide and protein level; their nucleotide sequences were expanded using blastn, as described for DjODC1 and DjODC2. In some cases, nucleotide sequences were fully expanded by comparison with a transcriptome assembled from sequence reads obtained from wild-type D. japonica . S. mediterranea ODC homologous sequences, were obtained by searching the Schmidtea mediterranea genome database (SmedGD) and the Planmine database. Dugesia japonica homologs of Smed-NB22.11.e, Smed-agat-2, Smed-Collagen, were obtained by BLAST analysis using as input S. mediterranea nucleotide sequences. Blastn and tblastx search were undertaken in D. japonica nucleotide collections/EST databases, and the transcripts with the highest similarity with those of S. mediterranea were taken, and called DjNB22.11.e (IAAB01021249.1, e-value: 2e-45 nucleotide identity 71%), DjAGAT2 (IAAB01039299.1, e-value: 3e-52, nucleotide identity 85%), and DjCollagen (IAAB01067699.1, e value: 0.0, nucleotide identity 81%) respectively. […]

Pipeline specifications

Software tools BLASTN, TBLASTX
Databases SmedGD PlanMine
Application Nucleotide sequence alignment