Sentence examples for using the emboss programs from inspiring English sources

To create this track a database of all possible ORFs longer than 45 bp was produced and translated into protein sequence using the EMBOSS programs.

The sites were mapped to 3 kb of promoter sequence of the β-catenin target genes using the Emboss program fuzznuc [31] allowing for 1 mismatch.

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].

Nucleotide sequence identities were calculated after the pairwise sequence alignment using the EMBOSS Water program (http://www.ebi.ac.uk/Tools/psa/emboss_water/nucleotide.html ).html

We aligned these protein sequences with human protein sequences using the Emboss Needle program (which implements the Needleman-Wunsch algorithm [ 27]) to extract identity, similarity and gap values for each rhesus protein model.

We identified uORFs and ncORFs longer than 10 aa with an AUG start codon followed by an in-frame stop codon within the annotated 5′-UTRs and ncRNA transcripts, using the emboss getorf program.

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

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].