Creating codon bias tables
MacVector is unable to create a codon bias table using the Make Entrez Codon Bias Table tool.
Use the BiasView application to format existing codon bias tables into MacVector format.
This problem is due to (1) the increasing size of the nucleic acid sequence databases and (2) a limit on the number of sequences that MacVector can use to create a codon bias table.
MacVector uses the NCBI Toolkit to handle communication with the NCBI servers. The Toolkit has a limit of 8191 on the number of sequences that it can retrieve. This limitation applies to retrieving sequences from Entrez as well as building codon bias tables.
An application called BiasView converts GCG format codon bias tables into a format that MacVector can use. This allows you to download tables from appropriate web sites (e.g. http://www.kazusa.or.jp/codon/) using your web browser and convert them with BiasView for use with MacVector.
BiasView is available on your MacVector distribution disk and as a Stuffit archive in the Downloads section of this website.
If the download is unavailable, please send an email to support@macvector.com and request this application for use with MacVector. BiasView will be emailed to you in a Stuffit archive. After opening the archive, please make sure that you read the readme file before using BiasView.
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