BOL: Related items

chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons.

Jit — Thu, 03 Feb 2022 04:01:55 -0600

chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons.

USAGE:

-query: sequence A in fasta format
-db: sequence B in fasta format
-out: output matrix
-kmer Integer: k>1 (default 32) Use 32 for chromosomes and genomes and 16 for small bacteria
-diffuse Integer: z>0 (default 4) Use 4 for everything - if using large plant genomes you can try using 1
-dimension Size of the output matrix and plot. Integer: d>0 (default 1000) Use 1000 for everything that is not full genome size, where 2000 is recommended

Address of the bookmark: https://github.com/estebanpw/chromeister

Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences

LEGE — Sun, 31 Aug 2025 06:30:16 -0500

Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.

Address of the bookmark: https://github.com/MGXlab/Jaeger

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/

ASAR: Advanced metagenomic Sequence Analysis in R

Jit — Mon, 09 Jul 2018 05:20:50 -0500

An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

Address of the bookmark: https://github.com/Askarbek-orakov/ASAR

medaka: Sequence correction provided by ONT Research

BioStar — Mon, 18 May 2020 16:28:00 -0500

medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.

Address of the bookmark: https://github.com/nanoporetech/medaka

Tools for Sequence translation !

Abhi — Tue, 08 Nov 2022 03:37:58 -0600

BOrf - https://github.com/betsig/borf

CodAn - https://github.com/pedronachtigall/CodAn

EMBOSS-Sixpack - https://www.ebi.ac.uk/Tools/st/emboss_sixpack/

esl-translate - http://hmmer.org/, https://github.com/EddyRivasLab/easel

GeneMarkS-T - http://exon.gatech.edu/GeneMark/license_download.cgi

ORFfinder - https://www.ncbi.nlm.nih.gov/orffinder/ (web server)

PLASS - https://github.com/soedinglab/plass

Prodigal - https://github.com/hyattpd/Prodigal

TransDecoder - https://github.com/TransDecoder/TransDecoder