Sentence examples for using the emboss dottup from inspiring English sources

Dot plot alignments were generated using the EMBOSS dottup program (Rice et al. 2000) with window size = 9 and step size = 1.

ORFs were identified by using the EMBOSS software (version 5.0.0; emboss.sourceforge.net).net

Alignments of the parent genes and CG proteins were generated using the Emboss Needle program (http://emboss.sourceforge.net/) with default options.

GC content was calculated using the EMBOSS geecee program.

(G + C) content was calculated using the eMBOSS geecee program http://inn-temp.weizmann.ac.il/cgi-bin/emboss/geecee[ 63].

Sequences were translated to amino acids using the Emboss Transeq web application [ 87].

Sequence analysis was performed using the Emboss software suite [ 37], Clustal W [ 38] and 3DCoffee [ 39].

Primer pairs were matched against bovine sequence from GenBank, NT and BTGI databases using the EMBOSS [ 26] primersearch tool.

Introns were assigned by aligning the unigenes with the melon genomic sequence using the Emboss: est2genome [ 105].

Secondary protein structure was predicted using the Emboss tool Garnier [ 78], whilst the tertiary protein structure prediction and 3D modeling were performed using Phyre2 [ 37] and ESyPred [ 38].

Self/self and all vs. all alignments of salamander intron sequences were performed using the program dottup (EMBOSS package) [ 58]. 427,188 bp of sequence from 48 axolotl introns was searched using several algorithms.