Molecular evolution of cyclin proteins in animals and fungi
- Equal contributors
1 Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
2 Novosibirsk state University, Pirogova, 2, Novosibirsk, Russia
BMC Evolutionary Biology 2011, 11:224 doi:10.1186/1471-2148-11-224Published: 28 July 2011
Additional file 1:
The packed archive contains files with multiple alignments of A-, B-, D-, and E- cyclin protein sequences in FASTA format.
Format: GZ Size: 52KB Download file
Additional file 2:
The packed archive contains files with gapless multiple alignments of A-, B-, D-, and E- cyclin proteins with reconstructed ancestors in FASTA format.
Format: GZ Size: 42KB Download file
Additional file 3:
The packed archive contains FASTA-like text files. Each text file contains space delimited numbers representing reconstruction probabilities of ancestral amino acids in internal tree nodes of A-, B-, D-, and E- cyclin phylogenetic trees for each ancestral sequence.
Format: GZ Size: 154KB Download file
Additional file 4:
The packed archive contains amino acid replacement matrices (in PAML format) for A-, B-, D-, and E- cyclin protein families. Each matrix file contains additional information for INDELIBLE simulations: the proportion of invariable sites; the shape parameter for the gamma distribution; the number of categories for use in the discrete gamma approximation.
Format: GZ Size: 3KB Download file
Additional file 5:
The packed archive contains MS Excel 2007 files. Each file represents the data on expected and observed number of amino acid replacements on each branch of the A-, B-, D-, and E- cyclin protein trees with probabilities p of its observation according to the stationary and homogeneous Markov model of protein evolution. These Excel files also contain the phylogenetic trees with ancestral node labels.
Format: GZ Size: 3.2MB Download file
Additional file 6:
The packed archive contains MS Excel 2007 files. Each file represents the following data: (1) the expected and observed numbers of amino acid replacements for each secondary structure element of animal A-, B-, B3-, D- and E-cyclins and fungal B-cyclins; (2) the probabilities p of its observation under the assumption that fixed replacements are distributed evenly in the protein.
Format: GZ Size: 364KB Download file
Additional file 7:
The packed archive contains Accelrys Discovery Studio *msv files. Each file contains 3D protein structure with mapped sites containing atypical amino acid replacements (in blue).
Format: GZ Size: 639KB Download file
Additional file 8:
MS Excel 2007 file contains the number of protein-protein interactions for different paralogs of the A-, B- D-, and E- cyclin proteins according to data deposited in the I2D (Version 1.72), HPRD (Release 8) and DroID (Version 5.0) databases.
Format: XLSX Size: 47KB Download file