Review of (ESPSearch)

Title: ESPSearch (version 1.01)


Date Reviewed: 17. May 2005

Description: search algorithm designed to locate specific target motifs in DNA, RNA, or protein sequences

Strengths: ESPSearch, from D.F.Doyle’s lab at Georgia Institute of Technology, is a complex search algorithm designed to identify specific target sequences in DNA, RNA, or protein sequences, such as direct repeats, 3 base triplets, and sequences containing many wildcards or gaps. It can also do pattern matching and identify specific a specific class of binding site such as transcription factors. Unlike BLAST, ESPSearch is not limited by length restrictions, wildcard constraints, variable regions, or specific mismatch levels. A number of target sequences, from 1 to 1000, can be searched simultaneously. The target sequences can be combined into one search and are user-determined. The program also has the advantage of being written in Python, a scripting language. Being a source code which can be edited by the user, the program can analyze user-specified patterns. There is an extensive user manual.

Weaknesses: Although the instruction manual appears comprehensive and a demonstration file is included on the home page of the web-site, there are no easily-identifiable instructions for using the program. This is also a relatively new program and limited application. Its operating speed might also be slower than comparable programs with specialized application,

Comprehensiveness: ESPSearch is a general tool for identifying any target within any source sequence. It is not a general alignment tool, such as BLAST. However, ESPSearch will locate sequences that BLAST cannot find.

Timeliness: (how often is the site updated)original release 1.10.05; current version 4.24.05.

Ease of Use: not certain, since I had trouble getting the demonstration file of the downloaded program to open

Responsiveness: (Do the pages download quickly?) yes, though actual program not readily identified

Similar or Related Sites: BLAST, TRANSFAC tools

Overall Evaluation: 1 to 5 stars ***

Reviewer: Peg Diffenderfer

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