Sentence examples for using the standalone package from inspiring English sources

GSEA [ 44] was performed using the standalone package (http://www.broadinstitute.org/gsea/) and genesets were taken from the MsigDB library [ 67].

These traces were downloaded and searched against our dataset using the standalone BLAST package (TBLASTx and TBLASTn algorithms with default gap costs and the BLOSUM62 matrix).

The pipeline aligned the T. biloba transcripts to D. melanogaster using the standalone BLAST package and a reference database available from FlyBase [ 49]. 11,008 transcripts from the meta-assembly were identified via BLAST as homologous to Drosophila sequences (44.9%).

Proteins from all genomes were blasted with the Arabidopsis protein queries (Additional file 3: Table S1) using the standalone BLAST software package.

Sequences were compared with the GenBank non-redundant (nr) protein database using the standalone Blastx program found in an executable package as previously described [ 40].

Computational predictions of localization were performed using the standalone version of PSORTb v.2.0 [ 31].

Protein family analyses were done using the standalone versions of PANTHER [ 67].

The ARACNE network was constructed using the aracne2 standalone software package according to authors instructions [ 40].

In addition, the standalone package and open source codes of WildSpan are now ready for downloading and can be used for large-scale proteome studies in the future.

Both the standalone package and online service are freely available at http://ibs.biocuckoo.org.

A user-friendly interface is provided in both the standalone package and online service of IBS.