Sequences were identified (Additional file 1: Table S1) using a BLAST search against the NCBI sequence database (National Center for Biotechnology Information, GenBank) to find the closest sequence matches in the database.
Using a blast search (http://blast.ncbi.nlm.nih.gov/Blast.cgi), the most genetically closest segment sequence is selected.
The obtained DNA sequences were investigated using a BLAST search as shown in Fig. 1A.
Homologs across species were established using a BLAST search against Rice, Poplar and Arabidopsis, considering sequence alignment coverage, best multi directional BLAST hits, sequence identity and protein domains.
Using a BLAST search, the sequence identity between CrSPI-1 and the most homologous member of the Kazal family of inhibitors was analyzed.
The three viral isolates studied were positive for JEV RNA; the JEV-positive samples were identified by RT-PCR using JEV-specific primers in NS1, C/prM and E regions and were matched to JEV using a BLAST search.
The remaining 166,352 reads (1.75%) were further analyzed using a BLAST search against non-redundant databases, revealing 80,827 (0.85%), 469 (0.005%), and 85,056 (0.90%) reads as influenza A virus, bacteria, and no hits, respectively (Fig. 1B).
If a single protein was submitted, similar sequences are gathered from a trimmed-down database of UniProt (version 14.3, [9]) protein sequences using a BLAST search (version 2.2.10, [10]).
The information of gene arrangement in chromosomes of five species that have the whole genome database (D. rerio, O. latipes, F. rubripes, T. nigroviridis and G. aculeatus) were accessed using a BLAST search through the UCSC [29] genome browser.
NC_005104) was identified using a BLAST search with stathmin1 cDNA sequence, and a 1.9 kb region corresponding −1534 to +325 was amplified by PCR using forward primer 5'- and reverse primer 5'- containing KpnI and NheI sites and subcloned into the KpnI-NheI site of the pGL3 basic vector.
