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By recognizing the formation and by reading the alignment and stances of the offensive linemen, Strahan was often able to anticipate the play before the ball was snapped.
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After scanning through all sequence reads, the alignment tool generates a file containing the collected information.
▪ Create perl scripts that read the alignment results and convert them to standard GFF3 format.
If another exact seed with smaller offset exists in the read the alignment is filtered as a duplicate, otherwise the alignment is recorded.
We then used the seqinr package [ 44] in R to read the alignments, and subsequently calculated gene-by-strain dN and dS values using the kaks command.
The receiver reads the defensive alignment and alters his pattern to run where the defender isn't.
For each read, the best alignment to the genome was kept in the output, with the exception of chimeric reads, for which multiple alignments were retained.
Once all the conversions are performed, a key aspect for the efficient alignment of the reads is the alignment strategy.
This reading of the alignment was included on the History Channel documentary, Decoding the Past.
As the sequencing was produced in a directed way, the reads alignment respects the strand of the DNA molecule.
The read alignment against the Ciona type A transcriptome was performed using the Burrows–Wheeler Alignment (BWA) tool (Li and Durbin 2009).
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