FASH: A web application for nucleotides sequence search

Isana Veksler-Lublinksy¹ , Danny Barash¹ , Chai Avisar¹ , Einav Troim¹ , Paul Chew² and Klara Kedem¹

¹Department of Computer Science, Ben-Gurion University, 84105 Beer-Sheva, Israel

²Computer Science Department, 721 Rhodes Hall, Cornell University, Ithaca, NY 14853, USA

author email corresponding author email

Source Code for Biology and Medicine 2008, 3:9doi:10.1186/1751-0473-3-9


Published:	27 May 2008

Abstract

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 webcite (secured website)