Reisner A H, Bucholtz C A
CSIRO, Division of Biotechnology, North Ryde, NSW, Australia.
Comput Appl Biosci. 1988 Aug;4(3):395-402. doi: 10.1093/bioinformatics/4.3.395.
Software has been developed to allow the use of a number of parameters in the comparative representation of proteins in color and monochrome dot matrices. They include the parameters of partial specific volume, residue bulkiness, the mean area buried of side chains, seven additional hydropathy scales, mutability, polarity, secondary structure propensities, energy/residue, energy/atom, Rf values, the pKs at the N and C terminals, user-defined parameters and, if desired, randomly generated values. Many of these parameters can be combined in n space using an algorithm based on the Euclidian distance relationship in order to derive consensus values. The problem of scoring matched identities is addressed and the user may stipulate that they score 100 on a 0-100 scale or be determined from the Dayhoff MDM78 values with the rest of the matrix scaled appropriately. The PAMs matrix has been incorporated in such a way to allow the user to stipulate various PAM's values or estimated percentage difference between two peptide sequences, and converting to log odds values. In addition, the similarity ring developed by Swanson and the matrix proposed by Bacon and Anderson have been adapted for use in the program. Color indices have been utilized to give a 'third dimension' to the projections, allowing the user to judge the degree of similarity of different regions which are represented. The software also provides for the plotting of nucleotides in which case color is used to code individual nucleotides, purines versus pyrimidines, or similar colors are used to differentiate between A and T bases on the one hand, and G and C on the other.
已开发出软件，可在彩色和单色点阵中对蛋白质进行比较表示时使用多个参数。这些参数包括比容、残基体积、侧链平均埋藏面积、七种额外的亲水性标度、可变性、极性、二级结构倾向、能量/残基、能量/原子、Rf值、N和C末端的pK值、用户定义的参数，以及如果需要的话，随机生成的值。其中许多参数可以在n维空间中使用基于欧几里得距离关系的算法进行组合，以得出共识值。解决了匹配同一性评分的问题，用户可以规定它们在0-100的量表上得分为100，或者根据Dayhoff MDM78值确定，同时矩阵的其余部分进行适当缩放。PAMs矩阵已被整合，以便用户规定各种PAM值或两个肽序列之间的估计百分比差异，并转换为对数几率值。此外，Swanson开发的相似性环以及Bacon和Anderson提出的矩阵已被改编用于该程序。颜色索引已被用于为投影提供“第三维度”，允许用户判断所表示的不同区域的相似程度。该软件还提供了核苷酸的绘图功能，在这种情况下，颜色用于编码单个核苷酸，嘌呤与嘧啶，或者使用相似的颜色来区分一方面的A和T碱基，以及另一方面的G和C碱基。
