ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets

Abstract

http://indra.mullins.microbiol.washington.edu/blast/viroblast.php.

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

“…The spacer sequences were BLASTed at the CRISPRTarget server against 'A CLAssification of Mobile genetic Elements (ACLAME)', 'Community Cyberinfrastructure for Advanced Microbial Ecology Research & Analysis (CAMERA)', phage, plasmid and viral databases (word match57, E-score51, match/mismatch51/21) (Biswas et al, 2013), at the ViroBLAST server against the viral databases (word match511, E-score510, match/mismatch score52/23) (Deng et al, 2007) and against the nucleotide collection database at the NCBI BLAST server (Altschul et al, 1997), using default settings for short sequences (word match511, E-value510). The top ten spacer hits from ViroBlast and NCBI BLAST servers were binned with a cut-off Identity-Cover (IC) score of 0.80.…”

Reconstructing the HIV-1 CRF02_AG and CRF06_cpx epidemics in Burkina Faso and West Africa using early samples

“…For the evolutionary analyses, we prepared 2 datasets: i) for a first analysis focused on Burkina Faso, we selected only sequences sampled in-country (130 PR and 39 gp41); ii) in a second analysis to explore the CRF02_AG spread throughout West Africa, we used all the selected sequences from West Africa together with the 5 closest sequences to each of them from Central Africa selected using ViroBLAST (Deng et al, 2007). Table 1 shows the number of CRF02_AG sequences included for each country in the definitive dataset, which included sequences sampled between 1993 and 2010 for the PR and between 1984 and 2009 for the gp41 gene.…”

Single-copy gene fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat

“…In barley, two copies of Acc-2 gene were found (Faris et al 2001). By comparing the wheat Acc-1 and Acc-2 cDNA sequences (AF029895 and U10187) against the genome sequence of barley (VIROBLAST (Deng et al 2007), http://webblast.ipk-gatersleben.de/barley/viroblast.php), we found one sequence with 95% similarity to wheat Acc-1 on barley chromosome arm 2HS and two sequences with 96% and 90% similarity to wheat Acc-2 on chromosomes arms 3HL and 5HL, respectively. Barley chromosomes are highly collinear to the corresponding wheat chromosomes (Dubcovsky et al 1996).…”