Sentence examples for using the emboss needle from inspiring English sources

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

All pairs of proteins were aligned using the EMBOSS needle program [ 23] and those with more than 30% sequence identity were connected in the paralogy network (see Methods).

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.

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

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].

Sequence manipulation was carried out using the EMBOSS suite of programmes [ 54].

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

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