FASH: A web application for nucleotides sequence search

: FASH (Fourier Alignment Sequence Heuristics) is a web application, based on the Fast Fourier Transform, for finding remote homologs within a long nucleic acid sequence. Given a query sequence and a long text-sequence (e.g, the human genome), FASH detects subsequences within the text that are remotely-similar to the query. FASH offers an alternative approach to Blast/Fasta for querying long RNA/DNA sequences. FASH differs from these other approaches in that it does not depend on the existence of contiguous seed-sequences in its initial detection phase. The FASH web server is user friendly and very easy to operate. Availability: FASH can be accessed at https://fash.bgu.ac.il:8443/fash/default.jsp (secured website) Background Recent discoveries [1] suggest that long RNA sequences, acting as natural sensors, exist in eukaryotic genomes and that such RNA sequences have not yet been found by commonly used bioinformatics methods. Although packages such as BLAST [2] and FASTA [3] are tremen...

• Type: Journal
• Year: 2008
• Where: SCFBM
• Authors: Isana Veksler-Lublinsky, Danny Barash, Chai Avisar, Einav Troim, L. Paul Chew, Klara Kedem
• Keywords: Fast Fourier Transform, Fourier Alignment Sequence, Rna Sequences, SCFBM 2008