Sentence examples for using the emboss package from inspiring English sources

The presence of recognized DNA binding motifs and active sites was assessed by using the Expasy site and PFAM bioinformatics algorithms available at http://us.expasy.org/cgi-bin/protscale.pl, and the electrostatic charge was calculated by using the EMBOSS package (http://proteas.uio.no/EMBOSS).uio.no/EMBOSS

Net charge of peptides was analyzed using the EMBOSS package pepstats (Rice et al. 2000).

The six-frame translation was achieved using the EMBOSS package (Rice et al., 2000).

A six frame translation (ORFs) from stop to stop for each assembled contig was generated using the EMBOSS package, version: 6.4.0.0 [ 39].

Preferred codons for each genome and codon adaptation index (CAI) (Sharp and Li 1987) for all genes were calculated using the EMBOSS package (Rice et al. 2000).

After using the EMBOSS package [ 24] to generate all possible open reading frames (ORFs) from stop to stop for each assembled contig, the resulting predicted ORFs were searched for sequence similarity against the N. vectensis proteome [ 25], using reciprocal BlastP (E-value ≤2e-30) [ 26] (Script 1).

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

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

The corresponding chimpanzee cDNA and protein sequences were extracted and compared to the human ortholog by using the EMBOSS sequence analysis package.

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.