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Old 03-16-2019, 01:26 AM   #1
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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
dineshkumarsrk is offline   Reply With Quote

bioinformatic analaysis, bioinformatics question, sequence alignment, tblastn

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