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.Ý It can also do pattern matching and identify specific a specific class of binding site such as transcription factors.Ý Unlike BLAST, ESPSearch is not limited by length restrictions, wildcard constraints, variable regions, or specific mismatch levels. ÝA number of target sequences, from 1 to 1000, can be searched simultaneously. ÝThe target sequences can be combined into one search and are user-determined. ÝThe program also has the advantage of being written in Python, a scripting language.Ý Being a source code which can be edited by the user, the program can analyze user-specified patterns.Ý There is an extensive user manual.Ý
Weaknesses:Ý 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.Ý This is also a relatively new program and limited application.Ý 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.Ý It is not a general alignment tool, such as BLAST.Ý 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 ÝÝÝ***
Reviewer: Peg Diffenderfer
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