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Old 03-16-2019, 01:26 AM   #1
dineshkumarsrk
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Location: India

Join Date: Mar 2019
Posts: 5
Question 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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