Table of Contents
What is an E value in BLAST?
The Expect value (E) is a parameter that describes the number of hits one can “expect” to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases. Essentially, the E value describes the random background noise.
How do you do a BLAST search sequence?
BLAST sequence similarity searching
- Select the ‘Blast’ tab of the toolbar at the top of the page to run a sequence similarity search with the Blast program.
- Enter either a protein or nucleotide sequence or a UniProt identifier into the form field (Figure 37).
- Click the ‘Run Blast’ button.
What’s the difference between BLASTn and blastx?
Blastx will search your sequence in a protein database with a nucleotide sequence as input while tblastn will search in a nucleotide database with a protein input.
What is NT in BLAST?
In this case, “nr” is non-redundant protein, “nt” is non-redundant nucleotide. Yes: you would blastn versus nt and blastp versus nr. No: you cannot BLAST both “at the same time.” You need to choose an appropriate combination of BLAST program and database.
How do I find my gene name in BLAST?
Go to the BLAST home page and click “nucleotide blast” under Basic BLAST. Paste the sequence in the query box, choose a database, and click the BLAST button. Click on the accession number of the desired sequence from the results and continue with step 4 in the “A Nucleotide Accession Number” section above.
What is blastn vs blastx?
When should I use blastn?
BLASTn (Nucleotide BLAST): compares one or more nucleotide query sequences to a subject nucleotide sequence or a database of nucleotide sequences. This is useful when trying to determine the evolutionary relationships among different organisms (see Comparing two or more sequences below).
What does NR mean in BLAST?
The nr database is compiled by the NCBI (National Center for Biotechnology Information) as a protein database for Blast searches. It contains non-identical sequences from GenBank CDS translations, PDB, Swiss-Prot, PIR, and PRF. The strengths of nr are that it is comprehensive and frequently updated.
What is NT and NR?
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.