In silico sequence and structure analysis for mycobacteriophages.


Rajendran, V.; Hassan, S.; Joseph, J.; Selvakumar, N.; Kumar, V.



Asian Pacific Journal of Tropical Biomedicine; 2012; S377-S379.


Abstract: Objective: To do a comparative homology search for the 32 mycobacteriophages.


Methods: This can be estimated as 3 400 proteins from 32 mycobacteriophages assuming each phage has 80-100 genes. The algorithm most widely used for homology detection in comparative genomics is Basic Local Alignment Search Tool (BLAST). Usually a stringent score cutoff is applied to distinguish putative homolog's from possible false positive hits. As a consequence, some BLAST hits are discarded or put into insignificant hits that are in fact homologous. Assigning function to protein sequences is important. Here, we review the status of sequence (BLAST) based and domain based approaches to proteins that can provide functional insights such as database on Protein Families (PFAM).


Results: The findings showed that 31% of proteins showed similarities with homologous protein with known function.


Conclusions: In the present study only 31% of mycobacteriophage proteins functions were able to be predicted. Only for 6 proteins, the template structures were available but then they were not directly involved in phage lifecycle. Hence this emphasizes the importance of exploring the structures for mycobacteriophage proteins in order to understand their function and evolutionary significance. Ab initio methods for protein structure prediction can be only alternative for the rest of the proteins but accuracy of prediction is not highly dependable.


Keywords: Mycobacteriophages; Comparitive genomics; BLAST; PFAM


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