BOL: Related items

Ancestral sequence reconstruction steps !

Surabhi Chaudhary — Fri, 18 May 2018 08:28:26 -0500

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?

1- Alignments "Mafft - http://mafft.cbrc.jp/alignment/software/source.html"

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.

- Tutorials: http://beast.bio.ed.ac.uk/tutorials

- Downloads: http://beast.bio.ed.ac.uk/downloads

Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore

Neel — Fri, 19 Oct 2018 08:48:43 -0500

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCONwhile producing contigs of comparable base accuracy.

Address of the bookmark: https://github.com/ruanjue/wtdbg2

MSAProbs - Parallel and accurate multiple sequence alignment

Neel — Tue, 09 Jul 2019 23:58:44 -0500

MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. In addition, MSAProbs is optimized for shared-memory CPUs by employing a multi-threaded design, and further parallelized for distributed-memory systems using MPI to overcome high memory overhead barrier and achieve good parallel and data-size scalability.

Address of the bookmark: http://msaprobs.sourceforge.net/homepage.htm#latest

Kalign: fast multiple sequence alignment program for biological sequences.

BioStar — Fri, 01 Nov 2019 00:20:41 -0500

Kalign is a fast multiple sequence alignment program for biological sequences.

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Address of the bookmark: https://github.com/TimoLassmann/kalign

AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

Jit — Sat, 01 Feb 2020 13:38:49 -0600

AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies

SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1911-0

Address of the bookmark: https://github.com/schneebergerlab/syri

flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Jit — Fri, 24 Apr 2020 08:39:28 -0500

FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and relaxed handling of mismatches and ambiguous residues. The custom shading modules facilitate dotplot interpretation and motif identification by adding information on sequence annotations and sequence similarities to the images. Combined with collage-like outputs, FlexiDot supports simultaneous visual screening of a large sequence sets, allowing dotplot use for routine screening.

Address of the bookmark: https://github.com/molbio-dresden/flexidot

LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data

Neel — Wed, 23 Jun 2021 07:54:53 -0500

LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads.

https://academic.oup.com/ve/article/7/1/veab042/6248116

Address of the bookmark: https://academic.oup.com/ve/article/7/1/veab042/6248116

UniAligner: a parameter-free framework for fast sequence alignment

Abhi — Fri, 08 Mar 2024 23:36:12 -0600

UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches, such as the Smith-Waterman algorithm, that work well for most sequences, fail to construct biologically adequate alignments of extra-long tandem repeats (ETRs), such as human centromeres and immunoglobulin loci. This limitation was overlooked in the previous studies since the sequences of the centromeres and other ETRs across multiple genomes only became available recently.

More at https://www.nature.com/articles/s41592-023-01970-4

Address of the bookmark: https://github.com/seryrzu/unialigner

Ribbon: Visualizing complex genome alignments and structural variation:

Jit — Wed, 29 Nov 2017 07:40:22 -0600

Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right.

Local installation:

You can install Ribbon locally from Github by following the instructions here: https://github.com/MariaNattestad/Ribbon

Address of the bookmark: http://genomeribbon.com/

jobTree based python wrapper to run the genome simulation tool suite Evolver

Jit — Fri, 08 Dec 2017 16:26:32 -0600

evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation as it runs including text and image files. Also included are convenience scripts to: check on a running simulation and see detailed status and logging information; extract fasta sequence files from the leaf nodes of a completed simulation; extract pairwise multiple alignment files (.maf) from leaf and branch nodes from a completed simulation and with the help of mafJoin, join them together into a single maf covering the entire simulation.

Address of the bookmark: https://github.com/dentearl/evolverSimControl