Blog of Andrés Aravena
Bioinfo:

# 4. How BLAST works?

09 November 2022

The key word here is index. BLAST uses an index to search for partial matches, or seeds, that are later extended using the local alignment matrix.

## Student 1 90

BLAST works by finding word-matches between the query and database sequences. And then it can initiate extensions. It is heuristic because searching sequences to compare with others is in the same consept [should be “concept”] with searching something where the light shines, not in the exact place of that thing. Even if we know the exact place of it; we are biologists, so we can’t search for things in the darkness. We need a light, in that case this light is a reference knowledge. So, BLAST compares our query with the knowledge it has from previous studies and sequencing results. Bu it only gives us the approximately answers, we need to change parameters to get more specific answers.

## Student 2 10

When we get a sequence that we don’t know what it is related to, we can upload this sequence to the BLAST and it compares this sequence with all sequences stored in its database. Also it can be a sequence that we know and we may want to learn how similar it is to a different sequence.

## Student 3 0

BLAST is a tool for local alignment. BLAST is useful for to compare two sequences, two proteins etc. BLAST doesn’t count external gaps and it finds to similar regions between query and subject and it gives us an E-value or an identity percentage. BLAST is heuristics because in BLAST we don’t find an exact result. We look for similarities or differences.

## Student 4 100

BLAST is a heuristic. It is more detailed search tool and it gives an approximate answer with lower cost. The heuristic algorithm of BLAST locates all common three-letter words between the sequence of interest and the hit sequence or sequences from the database. This result will then be used to build an alignment. After making words for the sequence of interest, the rest of the words are also assembled. These words must satisfy a requirement of having a score of at least the threshold T, when compared by using a scoring matrix.

## Student 5 50

BLAST finds high scoring local alignment between two sequences and includes a model of score distribution for random local alignment. BLAST works by sequencing the sequences of 2 living things locally. You need have some accession numbers or sequences that belong organism. And then choose another organism in the search tools and compare your sequence to other organism’s sequences.

## Student 6 50

BLAST is a basic local alignment tool. It compares the proteins or nucleotides. We enter a accesion number/FASTA sequences of our organism and then enter another accesion number/FASTA sequences. BLAST compare them in different databases and show results. But results are depends on E-Value. E-Values are depends on database. So it shows different approximate answers, it makes BLAST Heuristics.

The word is “accession”.

## Student 7 100

BLAST uses indices to look for an initial hit that is called seed). Then it tries to extend it using building a dot-matrix around the hit. The key parameter is word size. After finding a seed, BLAST must validate it. It is a heuristic. It gives the correct answer to a similar question and it gives an approximate answer.

## Student 8 100

BLAST uses indices to look for an initial hits. BLAST uses index for not making matrixes. First it uses index to find perfect subjects with many mismatch then it makes matrixes around that match. It misses some cases, it gives us approximate answer so it is heuristic.

## Student 9 100

BLAST uses indices to look for an initial hit or seed, then extends by building a dot matrix around it.

## Student 10 50

BLAST shows which sequences is similar our query in the databases. The query is the sequences of protein or accession number of protein and the subject is an organism that we will compare them.

## Student 11 90

BLAST is a heuristic that works by finding word matches between the sequences we want to compare (query) and database sequences.

## Student 12 40

Blast is a basic local alignment tool which means it allows us to compare genes to genes or protein to protein or protein in nucleotide database etc. It does local alignment between the selected query sequence and the database which is the subject. And after searching it, we achieve a similarity percentage between them, matching sequences information and else.

## Student 13 40

BLAST take query sequence (can be nucleotide or protein) and search it in a database (can be nucleotide or protein). And can align two or more sequences.

## Student 14 100

We give a query and BLAST searches for sequences that are similar. BLAST uses indices for an initial hit, then builds a matrix around to extend it. Also BLAST is heuristic, gives approximate answers.