Learn to use FASTA, a web-based tool for finding sequence similarities for proteins and nucleic acids. FASTA, one of the fastest sequence algorithms, optimizes searches for local alignments using a substitution matrix. Users can select their own parameters (or simply use the default choices) to find the best matches to their sequence. Results are displayed with alignments, scores, and visual graphics to help interpret the results. Sequences are also linked to annotated databases to provide additional biological knowledge.

You will learn:

  • the principles of sequence comparison and main features of the FASTA algorithm
  • basic explanations of scoring matrices and alignments
  • how to perform a sequence similarity search
  • how to view and interpret the similarity results
  • how to find additional biological information about matching sequences


This tutorial is a part of the tutorial group Alignment and comparison resources. You might find the other tutorials in the group interesting:

ClustalW2: Performs multiple sequence alignments

BLAST: Basic Local Alignment and Search Tool

Entrez Gene: NCBI's Entrez tool for gene-centric information

Primer3: Pick primers from a DNA sequence.

DCODE: DCODE.org Comparative Genomics Developments, a collection of powerful comparative genomics tools

VISTA: Tools for Comparative Genomics

RefSeq: Provides molecular sequence records to help locate gene and protein data.


EBI : This category includes all resources maintained at the European Bioinformatics Institute (EBI)

Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.


Tip of the Week: File Format conversion: Many of us have worked with DNA and protein sequences of course in several different formats: GenBank and FASTA to name two broadly used ones, but there are many others. Different tools and databases w...


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