Sentence examples for using the standalone blast from inspiring English sources

Sequence homology searches were performed using the standalone BLAST suite against D. melanogaster sequence databases (release 5.4) available in the FlyBase repository [ 66].

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).

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

For each simulation (idealized or randomized tree topologies), a BLASTP database including the protein sequences from all 100 genomes was created using the standalone BLAST program [ 17].

Comparative analyses of XccA306 and Xcaw12879 was conducted by, a two-way BLAST of the nucleotide sequences to identify unique genes in each strain using the standalone blast + software (ncbi-blast-2.2.4).

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%).

The β-keratin annotations were performed using the standalone BLAST+ program and the Greenwold and Sawyer [ 9] dataset as a database.

Type I and II α-keratin gene annotations were performed using the standalone BLAST+ program and the non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF database downloaded February 2013.

In order to verify these findings we downloaded all available EST libraries for the birds used in this study and used the standalone BLAST+ program and tblastn to search the expressed sequence tag (EST) libraries of the chicken (603,076 ESTs), turkey (17,435 ESTs), duck (5,249 ESTs), pigeon (4,931 ESTs) and zebra finch (92,142 ESTs).

All the BLAST searches have been performed using the standalone version of BLASTp program [ 21] obtained from NCBI by anonymous ftp (ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20051206).nih.gov/toolbox/ncbi_tools/old/20051206

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