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BLAST

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30 views2 pages

BLAST

Uploaded by

Filza Shareen
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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BLAST (Basic Local Alignment Search Tool) and FASTA are both bioinformatics tools

used for comparing biological sequences, such as DNA, RNA, or protein sequences.
Here’s a brief overview of each:

BLAST (Basic Local Alignment Search Tool)

 Purpose: BLAST is used to find regions of local similarity between sequences. It


compares a query sequence against a database of sequences and identifies matches
that share significant similarity.
 Types:
o BLASTN: For nucleotide sequences.
o BLASTP: For protein sequences.
o BLASTX: Translates nucleotide sequences into protein sequences and
compares them to protein databases.
o TBLASTN: Compares protein sequences against translated nucleotide
databases.
o TBLASTX: Compares the translated versions of nucleotide sequences
against each other.
 Output: The output includes information about the sequence matches, alignment
scores, E-values (expectation values), and graphical representations of the
alignments.
 Applications: It is commonly used for identifying homologous sequences, gene
discovery, and phylogenetic studies.

FASTA

 Purpose: FASTA is another sequence alignment tool, which can be used for both
local and global alignment of sequences. It is known for its speed, making it
suitable for large datasets.
 Features:
o FASTA uses a heuristic approach to align sequences, which generally
results in faster processing compared to other methods.
o It provides a scoring system based on similarity and gap penalties to assess
the quality of the alignments.
 Output: The results typically include alignment scores and a visual representation
of the alignment, showing matched and mismatched bases or residues.
 Applications: FASTA is often used for sequence comparison, database searching,
and multiple sequence alignments.

Comparison

 Speed: FASTA is generally faster than BLAST, especially for large databases, but
may be less sensitive in finding more distant homologs.
 Sensitivity: BLAST is often considered more sensitive for detecting similarities,
especially in large genomic datasets.
Usage in R

If you're using R for bioinformatics, you can leverage packages such as Biostrings from
Bioconductor for handling sequences and performing BLAST searches. For FASTA files,
the seqinr or Biostrings packages can also help with reading, writing, and manipulating
sequence data.

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