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  • #1

    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
    Tags: bioinformatic analaysis, bioinformatics question, sequence alignment, tblastn
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