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To exclude a rare possibility of different binding modes that can occur for a pair of homologous or even identical proteins, all pairs of obtained proteins are manually checked using subunit sequence similarity and symmetry information from 3D Complex.
This alignment was manually checked using BioEdit [ 33].
The sequence data were manually checked using SeqMan (DNASTAR).
All alignments were manually checked using BioEdit (Hall 1999).
Images were processed and manually checked using GenePix Pro 6.0/6.1 software.
MITE-Hunter outputs were manually checked using the approach described previously [ 23].
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Forward and reverse sequences were manually edited and checked using Bioedit v.7.0.5.2.
Using the BLAST tool, their current annotation status was manually checked against the Uniprot database [ 30], and their domain architecture checked using the Pfam domain organization database.
Gene predicted to be involved in functions of interest was manually checked by using the "genome browser" tool of the platform.
After SILVA-ngs analysis, the largest OTU of Cyanobacteria (containing 287 reads) detected at 3000 m were manually checked again using the web-BLASTn against the NCBI non-redundant nucleotide database.
Array images were manually checked for defects using DChip [20], [21] and then normalized using the RMA algorithm in Affymetrix Expression Console (v1.0).
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