Universal protein alignment (38 sequences)

This universal protein alignment is a concatenation of 56 proteins from 38 species

RNA stem alignment (125 sequences)

This alignment is a concatenation of rRNA stem sites from small and large rRNA subunits. It contains 125 sequences and is in Fasta format

Translational machinery of the chaetognath : a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression-4

<p><b>Copyright information:</b></p><p>Taken from "Translational machinery of the chaetognath : a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression"</p><p>http://www.biomedcentral.com/1471-2148/7/146</p><p>BMC Evolutionary Biology 2007;7():146-146.</p><p>Published online 28 Aug 2007</p><p>PMCID:PMC2020476.</p><p></p> for 37 different LSU RPs. The 28 nucleotides region of the sequence n°1 has been found in 75 ESTs putatively encoding for 25 different SSU RPs and in 96 ESTs putatively encoding for 29 different LSU RPs. The stars (*) indicate nucleotides which are conserved between these two sequences. The nucleotide regions which differ between these two sequences have been underlined and have named respectively TAC consensus site and TTT consensus site. The nucleotides which are conserved between these two consensus sites and Tinman/Nkx2.5 binding consensus sites are indicated in bold letters; K representing T or G

Translational machinery of the chaetognath : a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression-0

<p><b>Copyright information:</b></p><p>Taken from "Translational machinery of the chaetognath : a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression"</p><p>http://www.biomedcentral.com/1471-2148/7/146</p><p>BMC Evolutionary Biology 2007;7():146-146.</p><p>Published online 28 Aug 2007</p><p>PMCID:PMC2020476.</p><p></p> have been indicated for each cDNA type, TTT potential binding site(s) in black, TAT potential binding site(s) in white and partial sequences which do not contain the 5'-end in grey

Translational machinery of the chaetognath : a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression-1

<p><b>Copyright information:</b></p><p>Taken from "Translational machinery of the chaetognath : a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression"</p><p>http://www.biomedcentral.com/1471-2148/7/146</p><p>BMC Evolutionary Biology 2007;7():146-146.</p><p>Published online 28 Aug 2007</p><p>PMCID:PMC2020476.</p><p></p> for 37 different LSU RPs. The 28 nucleotides region of the sequence n°1 has been found in 75 ESTs putatively encoding for 25 different SSU RPs and in 96 ESTs putatively encoding for 29 different LSU RPs. The stars (*) indicate nucleotides which are conserved between these two sequences. The nucleotide regions which differ between these two sequences have been underlined and have named respectively TAC consensus site and TTT consensus site. The nucleotides which are conserved between these two consensus sites and Tinman/Nkx2.5 binding consensus sites are indicated in bold letters; K representing T or G

Translational machinery of the chaetognath : a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression-2

<p><b>Copyright information:</b></p><p>Taken from "Translational machinery of the chaetognath : a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression"</p><p>http://www.biomedcentral.com/1471-2148/7/146</p><p>BMC Evolutionary Biology 2007;7():146-146.</p><p>Published online 28 Aug 2007</p><p>PMCID:PMC2020476.</p><p></p>an amino acid dataset. The trees constructed using Fitch and MP methods have a similar topology. In D, the ML tree using the first two codon positions and the model selected by MrAIC, GTRIG, ML estimated base frequency, a gamma (2) distribution for site substitution rates, and an estimated proportion of invariant sites. Similar topologies were obtained with ML using codon models and with a non homogeneous non stationary ML method allowing G+C equilibrium frequency to vary (see text). Trees E and F were obtained using respectively the GTR model with a MCMC bayesian method and the CAT mixture model on an amino acid dataset. Numbers indicate bootstrap values or branch support; in tree B, MP and Fitch values are respectively at the left and at the right, in tree D, after the slash, the aLRT (actually the minimum of the CHI2-based parametric and non parametric aLRT estimated value). Abbreviations: D.m., ; Echino., Echinoderm; R.n., S.c., S.d., ; Yeast,

Additional file 2 of Assisted transcriptome reconstruction and splicing orthology

Results.tar. Compressed folder containing csv files listing the results. (GZ 3942 kb

Additional file 3 of Assisted transcriptome reconstruction and splicing orthology

TableS1. Data for Figure 3. (PDF 21 kb

Singh-BMCGenomics2009_NT_13proteins

Nucleotide concatenation of 13 mitochondrial protein-coding genes for 54 metazoan

Singh-BMCGenomics2009_AA_13proteins_CATBP

Bayesian consensus tree obtained under the CAT-BP mixture model using PhyloBaye