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Single nucleotide variants (SNVs) and indels in the tumor/normal pair were identified using a probabilistic joint variant calling approach utilizing SAMtools and Strelka [ 15, 16].
> The homologous proteins of members of species pair were identified using OrthoMCL version 2.0 (Li et al. 2003), and the transmembrane proteins among them were identified by using TMHMM 2.0 (Krogh et al. 2001).
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The homology between two exons in a pair was identified using the bl2seq implementation of TBLASTN.
For between genome comparisons, a pair of similar protein pair was identified using the reciprocal search method [ 36], i.e., the two proteins in the pair are the best hits in each other's genome from sequence search.
Matching pairs were identified using data collected from the two locations.
The 14N-/14N-labeled 14N-/14N-labeled 14N-/14N-labeled peptide pands were identified using pLink (Yang et al. 2015N-/15N-labeled 15N-/15N-labeled 15N-/15N-labeled
Similar review pairs were identified using paragraph level text comparisons.
P. anserina and N. crassa orthologous gene pairs were identified using FUNGIpath (Grossetete et al. 2010).
Duplicated gene pairs were identified using the four-fold degenerate transversion (4DTv) ratio calculated previously [ 23].
For RCT data sets, particle tilt pairs were identified using TiltPicker (Voss et al., 2009).
Duplicate read pairs were identified using Picard (http://picard.sourceforge.net/).net/
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