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The results were analyzed using analysis software on the website http://katahdin.mssm.edu/kismeth based on a previous report [ 43].
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The selection of the best-fit model of protein evolution for the CYP71C subfamily was done with ProTest software version 2.4 [ 33] based on protein alignment obtained with MUSCLE software (available on the website phylogeny.fr [ 34]) using the default parameters [ 35- 37].
For calculation purposes, we used the software available on the website of the University of Montreal (http://www.cpass.umontreal.ca/tcs.html).html
In order to ensure that sequences were not fragments or labeled incorrectly by protein family, sequences were analyzed using the SMART domain recognition software on the UniProtKB website.
The resulting peptide data from both mass and tandem mass were searched against SWISS-PROT database using MASCOT software on the matrixscience website (www.matrixscience.com).com
Interestingly, by alignment of the human and mouse promoter regions (−3000/0) of Cx43 with software on the NCBI website (http://blast.ncbi.nlm.nih.gov/Blast.cgi PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=align2seq), two conserved regions, −1064/−935 and −497/−1, in the human Cx43 gene were discovered.
Phylogenetic analysis was performed with the amino acid sequences of homologous genes from a wide variety of plant species registered in the NCBI and KEGG databases using ClustalW version 2.1 software on the DDBJ website (http://clustalw.ddbj.nig.ac.jp/index.php?lang=ja) in default mode.
The GPU-MCML code package has been released as an open-source software on this website: http://code.google.com/p/gpumcml.com/p/gpumcml
It is freely available over the web and can be incorporated in other tools through an http-based software interface described on the website.
Results, coverage reports and the used software package SCPSolver are available on the website http://www.ra.cs.uni-tuebingen.de/software/scpsolver/txp.
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