BOL: Related items

NCBI PSI-BLAST Tutorial

Fri, 23 Aug 2013 02:25:02 -0500

http:--www.biotechnology.jhu.edu- Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool and will protein and DNA sequences that are related to a sequence that the user provides.

Sequencing By Xpansion

Jitendra Narayan — Wed, 17 Jun 2015 20:58:11 -0500

Sequencing By Xpansion (SBX) is a DNA sequencing method that uses a simple biochemical reaction to encode the sequence of a DNA molecule into a highly measurable surrogate called an Xpandomer. This single molecule approach produces enough Xpandomer in a single drop reaction to sequence an entire human genome 1000X over. To achieve this, an Xpandomer replaces each DNA sequence with a sequence of large, high signal reporter molecules using the SBX molecular expansion technology. The DNA sequence is then read out as the Xpandomer reporters pass sequentially through a nanopore detector. SBX is a molecular engineering platform that benefits from core design principles that separate the multiple molecular functions. This systems approach enables efficient development and incorporation of improvements to SBX and is key to reconfiguring and optimizing Xpandomer measurement for different detection platforms.

http://www.stratosgenomics.com/stratos-genomics-technology

Blobsplorer

Jit — Tue, 14 Jun 2016 10:28:58 -0500

Blobsplorer is a tool for interactive visualization of assembled DNA sequence data ("contigs") derived from (often unintentionally) mixed-species pools. It allows the simultaneous display of GC content, coverage, and taxonomic annotation for collections of contigs with a view to separating out those belonging to different taxa.

Blobsplorer is unlikely to be of use on its own as it requires contig data to be supplied in a format that involves considerable preprocessing (see below for a description). The easiest way to use Blobsplorer is as part of a workflow using scripts from here.

Address of the bookmark: http://nematodes.org/martin/blobsplorer/blobsplorer.html

EAGER

Jit — Sat, 10 Dec 2016 18:07:23 -0600

The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.

EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0918-z

Address of the bookmark: https://github.com/apeltzer/EAGER-GUI

I-PV: Interactive Protein Sequence Visualization

Jit — Mon, 03 Jul 2017 07:52:51 -0500

I-PV is a interactive data visualization software designed for inspection of protein sequences and mutation information. It is mainly used for Genetics and Bioinformatics. So what exactly makes it standout?

http://i-pv.org/ipv_rec

Address of the bookmark: http://i-pv.org/

Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map

Jit — Wed, 11 Mar 2020 01:12:06 -0500

A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg)

Link to working demo: https://vgteam.github.io/sequenceTubeMap/

Address of the bookmark: https://github.com/vgteam/sequenceTubeMap

SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files

Rahul Nayak — Tue, 01 Mar 2022 03:13:33 -0600

A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. SeqFu is available for Linux and MacOS.

A compiled program delivering high performance analyses
Supports FASTA/FASTQ files, also Gzip compressed
A growing collection of handy utilities, also for quick inspection of the datasets

Can be easily installed via conda:

conda install -c bioconda seqfu

Address of the bookmark: https://telatin.github.io/seqfu2/

SeqCAT: Sequence Conversion and Analysis Toolbox

Neel — Fri, 14 Jun 2024 14:36:53 -0500

Your all-in-one solution for smooth conversion of sequence coordinates.

Designed for bioinformatics data analysis and daily laboratory work, SeqCAT simplifies sequence coordinate conversion. Extract gene and transcript information, manipulate sequences, and easily validate complex genetic events such as fusions with SeqCAT.

More at https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae422/7683049?login=false

Address of the bookmark: https://mtb.bioinf.med.uni-goettingen.de/SeqCAT/home

CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms

Jit — Tue, 25 Jul 2017 05:03:10 -0500

Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of different proteins, or the nucleotide sequences of different pieces of DNA. The Basic Local Alignment Search Tool (BLAST) has revolutionized the field of bioinformatics, and is currently implemented in all free and commercial bioinformatics packages. However, with the advent of Next Generation Sequencing (NGS) and the development of new sequencing techniques, the utility of traditional BLAST implementations is limited. CrocoBLAST combines the accuracy and general applicability of BLAST with computational efficiency, accessibility, and user experience, so that NGS data can be analyzed efficiently even when only modest computational resources are available.

https://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST

Address of the bookmark: https://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST

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/