Similar protocols

Pipeline publication

[…] b'om the blast2GO searches (blastx, tblastx and blastp; GO DB version: 2013\xe2\x80\x9309; E value < 10\xe2\x88\x925), public resources (UniProt, NCBI and GeneDB) and the referred publications. For the InterProScan and NCBI database searches, the information was obtained from the European Bioinformatics Institute - InterPro (http://www.ebi.ac.uk/interpro/) [] and the NCBI Conserved Domain Database (http://www.ncbi.nlm.nih.gov/cdd/) [], respectively., Protein coding sequences of F. hepatica transcripts were obtained using GETORF (http://emboss.bioinformatics.nl/cgi-bin/emboss/getorf), with the consideration of the frame sense and longest sequence length (n\xe2\x80\x89>\xe2\x80\x8930), and translated into amino acid sequences with Transeq (Jemboss; v1.5) []. The F. hepatica orthologous Dugesiidae sequences were determined with the blastx search based on the parasite\xe2\x80\x99s translated amino acid sequences (E value\xe2\x80\x89<\xe2\x80\x8910\xe2\x88\x923). Protein coding sequences of the Dugesiidae sequences were determined by GETORF with the same parameters and the sequences were trimmed from the ends to excise error letters (until the end letter, leaving the minimum sequence length of 18). The sequence alignment for each orthologous transcript was carried out with ClustalW (v2.1) [] using ParaAT (Parallel Alignment and back-Translation; version 1.0) []. The ratio for the number of nonsynonymous substitutions per nonsynonymous site (Ka) to the number of synonymous substitutions per synonymous site (Ks) for the aligned transcripts were estimated using KaKs_Calculator (version 1.2) [], with the MYN method (a modified version of the Yang-Nielsen algorithm [,]. For the remaining F. hepatica transcripts that are not orthologous to Dugesiidae or Ka/Ks ratio was not calculable, the Ka/Ks analysis was performed using the F. hepatica orthologous C. elegans sequences with the same approach. The P value for Ka/Ks ratio was calculated by the Fisher\xe2\x80\x99s exact test by ' […]

Pipeline specifications

Software tools TranSEQ, EMBOSS, BLASTX, Clustal W