Sentence examples for using the blast package from inspiring English sources

All nucleotide and predicted protein comparisons were performed using the BLAST package against the respective submitted C. jejuni genome updated nt and nr databases.

We used 5,176 orthologous gene pairs of human and mouse from the EBI database [ 33] and extracted reciprocal best-hit coding exon pairs using the BLAST package (version 2.2.11 from NCBI website).

Entry clones sequences were annotated based on the reference sequences using the Blast tools of the HUSAR software package [ 41].

Redundant sequences are identified using blastclust (part of the Blast package), using 95% identity and alignment length as search criteria.

Blast searches were performed using the blast program available at http://blast.ncbi.nlm.nih.gov.nih.gov

Using the local BLAST package from NCBI [ 42], we identified 9 contigs with high sequence coverage as elements of the cp genome.

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%).

Distinct sequences remaining after this analysis were subjected to an all-versus-all BLASTP comparison using the BLAST+ package, version 2.2.23, with default parameters used apart from an expectation value threshold of 1 × 10-3, and the use of soft masking of low-complexity regions.

Sma3s uses two programmes from the Blast package: blastp for amino acid sequences and blastx for nucleotide sequences, using an E-value threshold of 10−6, and blastclust for sequence clustering procedures.

The final fasta file that included all of the data was formatted using the formatdb program in the BLAST package [ 94].