BOL: Related items

PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool

Jit — Fri, 01 Dec 2017 04:10:54 -0600

PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.

Relying on unique software architecture, PLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

PLAST stands for Parallel Local Sequence Alignment Search Tool and is was published in BMC Bioinformatics.

PLAST is a general purpose sequence comparison tool providing the following benefits:

PLAST is a high-performance sequence comparison tool designed to compare two sets of sequences (query vs. reference),
Reduces the processing time of sequences comparisons while providing highest quality results,
Contains a fully integrated data filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.),
Does not require any additional hardware, since it is a software solution. It is easy to install, cost-effective, takes full advantage of multi-core processors and uses a small RAM footprint,
Ready to be used on desktop computer, cluster, cloud as well as within distributed system running Hadoop.

https://plast.inria.fr/

Address of the bookmark: https://plast.inria.fr/

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

AMStat: display statistics of large sequence files from next generation sequencing projects

Neel — Fri, 09 Nov 2018 13:34:56 -0600

SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a variety of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines.

Address of the bookmark: http://samstat.sourceforge.net/

TRITEX sequence assembly pipeline for Triticeae genomes

Jit — Tue, 20 Aug 2019 09:47:14 -0500

The pipeline is open-source and hosted in a public Bitbucket repository.

TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable results: super-scaffold N50 values in the range of dozens of Mb and pseudomolecules with better gene space representation than a BAC-by-BAC assembly. It has never been tested and is not expected to work on heterozygous or autopolyploid genomes.

A protocol for generating chromosome-conformation capture sequencing (Hi-C) data suitable for use with the pipeline is described in Himmelbach et al. 2018. Refer to the technical notes of 10X Genomics on how to generate Chromium data.

Address of the bookmark: https://tritexassembly.bitbucket.io/

Shouji: a fast and efficient pre-alignment filter for sequence alignment

Jit — Mon, 04 Nov 2019 07:09:45 -0600

The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes.

We introduce Shouji, a highly parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering accuracy by correctly detecting all common subsequences shared between two given sequences. The second key idea is to design a hardware accelerator design that adopts modern FPGA (field-programmable gate array) architectures to further boost the performance of our algorithm.

More at https://github.com/CMU-SAFARI/Shouji

Address of the bookmark: https://github.com/CMU-SAFARI/Shouji

CLARK: Fast, accurate and versatile sequence classification system

Jit — Sat, 15 Feb 2020 01:49:01 -0600

CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to known bacterial genomes, and (2) the assignment of BAC clones and transcript to chromosome arms/centromeres (in the absence of a finished assembly for the reference genome), CLARK outperforms in classification speed and precision the best state-of-the-art methods.

http://clark.cs.ucr.edu/Spaced/

Address of the bookmark: http://clark.cs.ucr.edu/Spaced/

RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler

LEGE — Thu, 09 Jul 2020 03:13:06 -0500

RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types:

single-end/paired-end bulk RNA-seq (strand-specific/agnostic)
paired-end single-cell RNA-seq (strand-specific/agnostic)
nanopore RNA-seq (PCR cDNA/direct cDNA/direct RNA)

Written by Ka Ming Nip ✉️

Address of the bookmark: https://github.com/bcgsc/RNA-Bloom

Kmer: a suite of tools for DNA sequence analysis

BioStar — Wed, 18 Aug 2021 00:02:54 -0500

More at https://help.rc.ufl.edu/doc/Kmer

This also includes:

A2Amapper: ATAC, Assembly to Assembly Comparision tool:
- Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).

Sim4db:
- Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.

LEAFF:
- LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.

Meryl:
- An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Address of the bookmark: https://help.rc.ufl.edu/doc/Kmer

Essentials of Statistics and Data Analysis using R

Mon, 31 Aug 2015 01:32:12 -0500

Clinical Development Services Agency (CDSA) is an extramural unit of Translational Health Science and Technology Institute (THSTI), Department of Biotechnology, Ministry of Science & Technology, Government of India. CDSA has a national mandate of strengthening capacity and capability building in the area of Clinical development and Translational Research.

CDSA is pleased to announce a 4 days hands-on training program on “Essentials of Statistics and Data Analysis using R” at ICGEB, Aruna Asaf Ali Road, New Delhi on December 1 – 4, 2015. This will involve developing and enhancing skills to understand basic principles of statistics for summarizing data and use of appropriate statistical tests as well as providing an understanding of data analysis using R. Didactic lectures with practical sessions will be delivered by experienced faculties from AIIMS and Novartis. Live classroom with power point presentations, case studies, mock exercise, practical sessions on R, group work with time for discussion and Q&A sessions are added advantages of this workshop.

Please contact gayatrivishwakarma.cdsa@thsti.res.in or vineetabaloni.cdsa@thsti.res.in for program and registration details.

Please nominate personage or register yourself on or before November 6, 2015 along with the electronic transfer of registration fee.

A web-based tool for sequence alignment statistics and innovative visualization

BioStar — Thu, 04 Apr 2024 01:44:50 -0500

AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/