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Briefings in Bioinformatics 2004 5(1):82-87; doi:10.1093/bib/5.1.82
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© Henry Stewart Publications

Software review

Analysis for free: Comparing programs for sequence analysis

Helge-Friedrich Tippmann
Plant Research Department, Risø National Laboratory DK-4000 Roskilde, Denmark Tel: 0045 4677 4291 E-mail: helge.tippmann{at}tu-berlin.de

Programs to import, manage and align sequences and to analyse the properties of DNA, RNA and proteins are essential for every biological laboratory. This review describes two different freeware (BioEdit and pDRAW for MS Windows) and a commercial program (Sequencher for MS Windows and Apple MacOS). Bioedit and Sequencher offer functions such as sequence alignment and editing plus reading of sequence trace files. pDRAW is a very comfortable visualisation tool with a variety of analysis functions. While Sequencher impresses with a very user-friendly interface and easy-to-use tools, BioEdit offers the largest and most customisable variety of tools. The strength of pDRAW is drawing and analysis of single sequences for priming and restriction sites and virtual cloning. It has a database function for user-specific oligonucleotides and restriction enzymes.

Keywords: sequence comparison tools, alignment, annotation, freeware, sequence analysis


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