Similar protocols

Protocol publication

[…] s, suggests a P-value of 1 – (1 − 0.05)1/24, or about 0.0021, where 0.05 is the original level of significance and 24 is the number of comparison tests performed. This assumes that the genes and their products are independent – there does not appear to be any evidence that a mutation in one FA protein leads to the absence of any of the other FA proteins., Protein structural models ( and ) were constructed using Discovery Studio v. 3.1 (BIO-VIA), based on pdb files in the RCSB Protein Data Bank, using 50 iterations with loop refinement. The protein motif diagrams were based on the information in Pfam 29.0., Full protein sequences (see Supple mentary for accession numbers) were aligned using MAFFT with default settings. Poorly aligned regions were excised using TrimAI v. 1.3 using the Gappyout setting on the Phylemon 2.0 web server. RAxML v. 8.0.0 was used to construct a maximum likelihood (ML) tree with bootstrap number determined with the FC bootstrapping criterion and PROTGAMMABLOSUM62 substitution model. User supplied trees with candidate genes rearranged were statistically evaluated using the Shimodaira–Hasegawa (SH) log likelihood test in RAxML., Our analysis revealed that Ciona has highly conserved orthologs of genes from each of the three FA protein groups (). Like all the other multicellular organisms examined, Ciona has both members of group II: FANCD2 and FANCI. However, only 4 of 9 members of group I and 5 of 8 members of group III were found, as well as only 2 of several “FA associated” proteins. In fact, Ciona appears to have as few or fewer members of the FA pathway of any multicellular organism examined, including plants, slime mold, and the primitive metazoan Nematostella., Below we present evidence for or against orthology in C. intestinalis of each of the members of the FA pathway. The first analyses described ar […]

Pipeline specifications

Software tools MAFFT, Phylemon, RAxML