Title

A Novel Index To Identify Unbiased Conservation Between Proteomes

Keywords

Bioinformatics; Chloroplast; Conservation

Abstract

As more genomes are sequenced, their comparative analysis helps to identify conservation between them which provides evidence on the evolutionary history of organisms. Since organisms and organellar genomes/proteomes exhibit significant differences in size and complexity, the comparative analysis requires an appropriate approach to detect an unbiased degree of conservation among them. In order to increase the significance of similarity search, we defined three new parameters; Cumulative Sum of Homologs (CSH), Actual Proportion of Homologs (APH) and Homology Impact (HI) for post BLAST analysis. These parameters were tested using complete chloroplast proteomes and two separate comparisons, one of Poales (similar group) and other of several diverse groups (including algae, bryophytes, pteridophytes, gymnosperms and angiosperms) were performed. The number of proteins among these chloroplast proteomes range between 64 and 367. These parameters can be used to evaluate the results of comparative sequence analysis of other organisms' proteomes using other similarity search tools. Comparison of chloroplast proteomes of similar and diverse organisms shows common and lineage specific conservation. Based on complete chloroplast proteome analysis using CSH, APH and HI, we identified Charales as sister and bryophytes as a basal clade of land plants which validates all three parameters. In addition, our results also support hornworts as the transition link between bryophytes and pteridophytes. Our overall analysis suggests that the above defined parameters are useful to identify unbiased conservation between proteomes. ©IJIB, All rights reserved.

Publication Date

11-11-2009

Publication Title

International Journal of Integrative Biology

Volume

7

Issue

1

Number of Pages

32-38

Document Type

Article

Personal Identifier

scopus

Socpus ID

70350764830 (Scopus)

Source API URL

https://api.elsevier.com/content/abstract/scopus_id/70350764830

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