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Related Experiment Videos

FASH: A web application for nucleotides sequence search.

Isana Veksler-Lublinksy1, Danny Barash, Chai Avisar

  • 1Department of Computer Science, Ben-Gurion University, 84105 Beer-Sheva, Israel. klara@cs.bgu.ac.il.

Source Code for Biology and Medicine
|May 29, 2008
PubMed
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Fourier Alignment Sequence Heuristics (FASH) is a web tool for identifying distant genetic similarities in long DNA or RNA sequences. It offers an alternative to BLAST and FASTA, excelling with large genomes.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Identifying remote homologous sequences is crucial for understanding gene function and evolution.
  • Existing tools like BLAST and FASTA have limitations when querying very long nucleic acid sequences, particularly regarding contiguous seed sequences.

Purpose of the Study:

  • To introduce FASH (Fourier Alignment Sequence Heuristics), a novel web application for detecting remote homologs in long nucleic acid sequences.
  • To provide a user-friendly alternative to BLAST/FASTA for analyzing large-scale genomic data.

Main Methods:

  • FASH utilizes the Fast Fourier Transform (FFT) algorithm for sequence alignment.
  • The method detects subsequences with remote similarity to a query sequence within a larger text sequence.

Related Experiment Videos

  • Unlike traditional methods, FASH does not rely on identifying contiguous seed sequences in the initial detection phase.

    • Main Results:

    • FASH successfully identifies remotely similar subsequences within long nucleic acid sequences.
    • The application provides an alternative approach to established sequence alignment tools for large datasets.

    Conclusions:

    • FASH offers a powerful and accessible web-based solution for remote homology detection in genomics.
    • Its unique approach, based on FFT and not requiring seed sequences, expands the capabilities for analyzing long RNA and DNA sequences.