Learning Resource Center: Introduction to NCBI Bioinformatics Resources: BLAST Results (2024)

FAQs

How to interpret NCBI BLAST results? ›

Blast results are sorted by E-value by default (best hit in first line). The smaller the E-value, the better the match. Blast hits with an E-value smaller than 1e-50 includes database matches of very high quality. Blast hits with E-value smaller than 0.01 can still be considered as good hit for hom*ology matches.

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. This means the two sequences must match with at least 11 nucleotides for blastn to be able to report any hit at all.

Access the “Protein–protein BLAST (blastp)” page by clicking on the link, paste in the query sequence, select the Swissprot database from the “Choose database” pull down menu and click on the BLAST! link. For each protein–protein search, the query is also searched against the Conserved Domain Database (see Note 5).

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.

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.

Max[imum] Score: the highest alignment score calculated from the sum of the rewards for matched nucleotides or amino acids and penalities for mismatches and gaps.

e values of 0 mean that there's an exact match for you sequence here... mike. -jadefalcon- e-values in blast results represent the probability of the alignment occurring by chance. It is a statistical calculation based on the quality of alignment (the score) and the size of the database.

For the purposes of the initial triage, a high Identity value generally falls in the range of 98-100% sequence similarity. The identity reports on the percentage of base pairs that are the same between the sequence of your specimen and that of the reference specimen.

Main steps of BLAST

Step 1: Given query sequence Q, compile the list of possible words which form with words in Q high scoring word pairs. Step 2: Scan database for exact matching with the list of words complied in step 1. Step 3: Extending hits from step 2. Step 4: Evaluating significance of extended hits from step 3.

What does E value mean in NCBI BLAST? ›

Q: What is the Expect (E) value? 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.

BLAST Scores and Statistics

The bit score gives an indication of how good the alignment is; the higher the score, the better the alignment.

BLAST uses statistical theory to produce a bit score and expect value (E-value) for each alignment pair (query to hit). The bit score gives an indication of how good the alignment is; the higher the score, the better the alignment.

Max[imum] Score: the highest alignment score calculated from the sum of the rewards for matched nucleotides or amino acids and penalities for mismatches and gaps.

Total score = sum of alignment scores of all segments from the same database sequence that match the quary sequence（calculated over all segments）. This score is different from the max score if several parts of the database sequence match different parts of the query sequence.

Positives. In the context of alignments displayed in BLAST output, positives are those non-identical substitutions that receive a positive score in the underlying scoring matrix, BLOSUM62 by default. Most often, positives indicate a conservative substitution or substitutions that are often observed in related proteins.

Bit score is a normalized score and hence it is independent of the size of the database, while E- values are very sensitive to the database size. Generally, bit scores of 40 or higher are considered reliable.

Max score: the highest bit score that is calculated from alignment matches and mismatches. The bit-score is the required size of a sequence database in which the current match could be found by chance. It is derived from the raw alignment score; the higher the score, the better the alignment.

Max[imum] Score: the highest alignment score calculated from the sum of the rewards for matched nucleotides and penalities for mismatches and gaps. Total Score: the sum of alignment scores of all segments from the same subject sequence.

The BLAST E-value is the number of expected hits of similar quality (score) that could be found just by chance. E-value of 10 means that up to 10 hits can be expected to be found just by chance, given the same size of a random database.

What is the importance of BLAST in bioinformatics? ›

BLAST is a computer algorithm that is available for use online at the National Center for Biotechnology Information (NCBI) website, as well as many other sites. BLAST can rapidly align and compare a query DNA sequence with a database of sequences, which makes it a critical tool in ongoing genomic research.

similarity. The extent to which nucleotide or protein sequences are related. Similarity between two sequences can be expressed as percent sequence identity and/or percent positive substitutions. SEG.