<![CDATA[BOL: Surabhi Chaudhary's pages]]> https://bioinformaticsonline.com/pages/owner/surabhi? https://bioinformaticsonline.com/pages/view/36711/ancestral-sequence-reconstruction-steps Fri, 18 May 2018 08:28:26 -0500 https://bioinformaticsonline.com/pages/view/36711/ancestral-sequence-reconstruction-steps <![CDATA[Ancestral sequence reconstruction steps !]]> Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolution. The method consists of the synthesis of an ancestral gene and expression of the corresponding ancestral protein. The idea of protein 'resurrection' was suggested in 1963 by Pauling and Zuckerkandl. Some early efforts were made in the eighties-nineties, led by the laboratory of Steven A. Benner, showing the potential of this technique – one that only started to be fulfilled in the post-genomic era. Thanks to the improvement of algorithms and of better sequencing and synthesis techniques, the method was developed further in the early 2000s to allow the resurrection of a greater variety of and much more ancient genes. Over the last decade, ancestral protein resurrection has developed as a strategy to reveal the mechanisms and dynamics of protein evolution. 
 
BEAST is the best way to predict the ancestral structure. but, I suggest following steps?
 
mafft --maxiterate 1000 --reorder --thread 24 --genafpair Dataset.fasta > Dataset_Alig.fasta
 
2- Your dataset has a good phylogenetic signal, is possible to perform with Tree-Puzzle "http://www.tree-puzzle.de";
 
3 - This dataset which the saturation index, I perform with "http://dambe.bio.uottawa.ca/dambe.asp";
 
4- Has evidence of possible recombination in your dataset, the evaluate if this presence or absence, because this may to influence the grouping of clades, I perform with
---recombination
 
4.1- Phi-test, implemented in SplitTree4"http://www.splitstree.org", (.nex file)
 
4.2- GARD deployed in webserver in the DataMonkey "http://www.datamonkey.org/" - turning to the amino acid seaview -> view proteins -> save as ...) Ideally do a tree-based groups.
 
4.3- RDP4 for download and installation on Windows in "http://web.cbio.uct.ac.za/~darren/rdp.html"
 
4.4- Hyphy (Mac, Windows, Linux) in "http://hyphy.org/w/index.php/Download"
 
4.5- Path-o-Gen (temporal structure of a tree input file -> arquivo.tre)
These steps above, I call of pre-processing to inferences phylogenetic...
 
5- Perform phylogenetic tree, used Bayesian Inference with Molecular Clock, but is necessary Clock Testing:
 
- This step is performed with program Beast (Beauti, Beast and TreeAnnotator), and Tracer_v1.5 more FigTree to inspection.
 
]]> Surabhi Chaudhary