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-   -   How to specify/calculate subject coverage in tBLASTn (http://seqanswers.com/forums/showthread.php?t=88201)

dineshkumarsrk 03-16-2019 01:26 AM

How to specify/calculate subject coverage in tBLASTn
 
I have been screening the homologous gene sequences from my genome of interest by doing tBLASTn, wherein I have to specify two mandatory parameters such as,
Coverage = 40% and Percentage of identity = 70%
Percentage of identity can be specified or derived from the tabular out put format (-outfmt 6). Since tBLASTn analyse, protein against nucleotide hits, therefore how to calculate the coverage percentage of the same. if i manually calculate the coverage percentage, its so tedious (3 nucleotide to 1 amino acid formula) process. Moreover, I have to carry out this analysis for numerous genomes. Hence, please suggest me any strategy to do the same.
Thank you in advance:)


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