Estimating the fraction of invariable codons with a capture-recapture method

✍ Scribed by Arend Sidow; Trang Nguyen; Terence P. Speed

• Publisher: Springer
• Year: 1992
• Tongue: English
• Weight: 677 KB
• Volume: 35
• Category: Article
• ISSN: 0022-2844
• DOI: 10.1007/bf00178601

✦ Synopsis

A codon-based approach to estimating the n u m b e r of variable sites in a protein is presented. When first and second positions of codons are assumed to be replacement positions, a capture-recapture model can be used to estimate the n u m b e r of variable codons from every pair of homologous and aligned sequences. The capture-recapture estim a t e is c o m p a r e d to a m a x i m u m likelihood estimate of the n u m b e r of variable codons and to previous approaches that estimate the n u m b e r of variable sites (not codons) in a sequence. C o m p u t e r simulations are presented that show under which circumstances the capture-recapture estimate can be used to correct biases in distance matrices. Analysis of published sequences of two genes, calmodulin and serum albumin, shows that distance corrections that e m p l o y a capture-recapture estimate of the n u m b e r of variable sites m a y be considerably different f r o m corrections that assume that the n u m b e r of variable sites is equal to the total n u m b e r of positions in the sequence.