How do you reference BLAST tool?

For the command-line version of NCBI BLAST, and for details of the BLAST method, you would cite:

1. Camacho C. et al.
2. Altschul S.F. et al. (1997) “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs”
3. Altschul S.F. et al. (1990) “Basic local alignment search tool”

What databases does BLAST use?

The original BLAST program used a protein “query” sequence to scan a protein sequence database. A version operating on nucleotide query” sequences and a nucleotide sequence database soon followed.

What is BLAST database?

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.

What does NR NT stand for in BLAST?

non-redundant nucleotide
In that case, “nr/nt” stands for “non-redundant nucleotide.” However, as you point out, NCBI also make separate databases available for download. In this case, “nr” is non-redundant protein, “nt” is non-redundant nucleotide.

What is the difference between Blastn and Blastp?

Blastn is in fact a rather poor tool for finding protein-coding sequences. The amino acid sequences being identical, blastp would have no problem in retrieving one sequence, using the other sequence as query. Blastn, however, uses a default word size of 11 nucleotides.

How do I read my blast results?

The list of hits starts with the best match (most similar). E-value: expected number of chance alignments; the smaller the E-value, the better the match. First in the list is the query sequence itself, which obviously has the best score.

Are Blastn results always correct?

BLAST is a heuristic program, not guaranteed always to find the optimal alignments, and scaling or adjusting the substitution matrix separately for each database sequence would unduly increase execution time. Accordingly, we re-evaluate only those database sequences which pass an initial screen.

How does blast work to find local alignment?

Learn more. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.

How to use Delta blast to search databases?

DELTA-BLAST constructs a PSSM using the results of a Conserved Domain Database search and searches a sequence database. Maximum number of aligned sequences to display (the actual number of alignments may be greater than this). Automatically adjust word size and other parameters to improve results for short queries.

What is blast and how does it work?

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences…

How does blast calculate the significance of a match?

The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.