VBLAST: Customized BLAST Search for Vaccine Research
VIOLIN provides 5 customed, pathogen specific BLAST searches:
- Regular BLAST
-- Include blastn, blastp, blastx, tblastn, tblastx.
- PSI/PHI BLAST
-- Position Specific Iterated (PSI) BLAST: Search databases of sequence profiles to find members of the same protein family. First, run BLAST and construct a position-specific score matrix (PSSM) from significant hits; then use this PSSM to query profile databases. PSI BLAST uncovers more distant protein relationships.
-- Pattern Hit Initiated (PHI) BLAST: Identify proteins that preserve a specified pattern contained within your query. Query includes a protein sequence and a regular expression defining the pattern of interest.
- Mega BLAST
-- NCBI'zed version of Webb Miller et al's greedy algorithm of nucleotide sequence alignment search. Mega BLAST is optimized for aligning sequences that differ slightly as a result of sequencing or other variations. It is approximately 10 times faster than more common sequence similarity programs and therefore can be used to swiftly compare two large sets of sequences against each other.
- RPS BLAST
-- Reversed Position Specific (RPS) BLAST:
compare a sequence to a collection of conserved domains (e.g., motifs, profiles, HMMs). RPS Blast has an option to perform a translated search of DNA sequences against these conserved domains. RPS Blast is the basis for the CDD Blast search page.
Note: new library is to be built.
- BLAST 2 sequences
-- BLAST 2 uploaded or pasted sequences against each other.
- Readme file
Statisitcs: The BLAST libraries are built on the sequences from 77 genomes of 34 pathogens. The BLAST libraries stores 211987 pathoen gene sequences, 201748 pathoen protein sequences, and 7938 PSSMs. The BLAST libraries also includes 94 vaccine-realted gene sequences and 80 vaccine-related protein sequences.
Provenance: All the data in the BLAST libraries are originally obtained from NCBI RefSeq database. These BLAST libraries are prepared by PHIDIAS following the BLAST's instruction.
