BOL: Related items

HistoneDB 2.0 – with variants

Anjana — Fri, 03 Jun 2016 05:06:20 -0500

This histone database can be used to explore the diversity of histone proteins and their sequence variants in many organisms. The resource was established to better understand how sequence variation may affect functional and structural features of nucleosomes. To get started, select a histone type to explore its variants.

More at http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

Address of the bookmark: http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

GOLD:Genomes Online Database

Jit — Wed, 26 Jul 2017 07:49:29 -0500

GOLD:Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.

https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

HIV genome database !

Rahul Nayak — Fri, 21 Jan 2022 05:40:15 -0600

HIV resources

https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html

Address of the bookmark: https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html

Enzyme Portal

Rahul Agarwal — Tue, 03 Sep 2013 18:06:06 -0500

Enzyme Portal- To look for information about the biology of a protein with enzymatic activity.

The enzyme portal integrates many resources, most of them hosted by EBI and also external ones such as BioPortal. Its main goal is to provide information about enzymes in a suitable format, with a usable interface designed for intended users. Instead of reinventing the wheel, it makes use of available and reliable resources to that end.

Related Literature:

http://nar.oxfordjournals.org/content/41/D1/D773.full

http://www.biomedcentral.com/1471-2105/14/103

Address of the bookmark: http://www.ebi.ac.uk/enzymeportal/

HumCFS: a database of fragile sites in human chromosomes

Abhimanyu Singh — Sun, 21 Apr 2019 20:17:29 -0500

Fragile sites are specific chromosomal region that exhibit an increased frequency of chromosdomal breakge when cells are exposed to replicative stress. Since from the discovery of chromosomal fragile sites/regions (CFS), several line of evidence suggests their involvement in human pathologies and they have been recognized as a preferential site for integration of exogenous oncogenic DNA viruses and hotspots for chromosomal re-arrangement. There is large gap in our knowledge of human CFS region as knowledge about CFS are unequally distributed in literature, which impose a problem in studying these region. In order to address these issues, we develop this platform HumCFS, which provides comprehensive information about experimentally identified CFS at a single source.

https://link.springer.com/epdf/10.1186/s12864-018-5330-5?author_access_token=ICASEpyMAQaxLlKw--fyCG_BpE1tBhCbnbw3BuzI2RMA57KLmXk5bZabRUiDQzRFHXd6hjm4kWSiLV3mU5XVMitqXUwFMSo4x5vbfty0EDQ9PW1sd1h923_TYXkvJ5niSwAyZ7BklJ0ujFAFhcKtjw%3D%3D

Address of the bookmark: https://webs.iiitd.edu.in/raghava/humcfs/

genomics public data links !

Jit — Thu, 13 Feb 2020 00:20:00 -0600

List of publically available databases on google server.

More at https://software.broadinstitute.org/gatk/download/bundle

ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.

ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/

Address of the bookmark: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

ncbi-datasets-cli -- Quickstart: command line tools !

Jit — Tue, 07 Dec 2021 02:51:26 -0600

Install and use the NCBI Datasets command line tools

The NCBI Datasets datasets command line tools are datasets and dataformat .

Use datasets to download biological sequence data across all domains of life from NCBI.

Use dataformat to convert metadata from JSON Lines format to other formats.

Conda download:

https://anaconda.org/conda-forge/ncbi-datasets-cli

Buld Download

https://www.ncbi.nlm.nih.gov/datasets/builder/?tax_id=29979

Address of the bookmark: https://www.ncbi.nlm.nih.gov/datasets/docs/v1/quickstarts/command-line-tools/

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

Jit — Wed, 06 Dec 2017 02:08:14 -0600

An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.

Address of the bookmark: ftp://ftp.genomics.org.cn/pub/cope

Musket - a multistage k-mer spectrum based corrector

BioStar — Tue, 04 Feb 2020 23:24:57 -0600

Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage workflow. Our performance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal that Musket is consistently one of the top performing substitution-error-based correctors.

Address of the bookmark: http://musket.sourceforge.net/homepage.htm

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies

Jit — Fri, 06 Jul 2018 03:36:45 -0500

KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT:

hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in output for easy plotting.
gcp: K-mer GC Processor. Creates a matrix of the number of K-mers found given a GC count and a K-mer count.
comp: K-mer comparison tool. Creates a matrix of shared K-mers between two (or three) sequence files or hashes.
sect: SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.
blob: Given, reads and an assembly, calculates both the read and assembly K-mer coverage along with GC% for each sequence in the assembly.SEquence Coverage estimator Tool.
filter: Filtering tools. Contains tools for filtering k-mer hashes and FastQ/A files:
- kmer: Produces a k-mer hash containing only k-mers within specified coverage and GC tolerances.
- seq: Filters a sequence file based on whether or not the sequences contain k-mers within a provided hash.
plot: Plotting tools. Contains several plotting tools to visualise K-mer and compare distributions. The following plot tools are available:
- density: Creates a density plot from a matrix created with the "comp" tool. Typically this is used to compare two K-mer hashes produced by different NGS reads.
- profile: Creates a K-mer coverage plot for a single sequence. Takes in fasta coverage output coverage from the "sect" tool
- spectra-cn: Creates a stacked histogram using a matrix created with the "comp" tool. Typically this is used to compare a jellyfish hash produced from a read set to a jellyfish hash produced from an assembly. The plot shows the amount of distinct K-mers absent, as well as the copy number variation present within the assembly.
- spectra-hist: Creates a K-mer spectra plot for a set of K-mer histograms produced either by jellyfish-histo or kat-histo.
- spectra-mx: Creates a K-mer spectra plot for a set of K-mer histograms that are derived from selected rows or columns in a matrix produced by the "comp".

In addition, KAT contains a python script for analysing the mathematical distributions present in the K-mer spectra in order to determine how much content is present in each peak.

This README only contains some brief details of how to install and use KAT. For more extensive documentation please visit: https://kat.readthedocs.org/en/latest/

https://academic.oup.com/bioinformatics/article/33/4/574/2664339

Address of the bookmark: https://github.com/TGAC/KAT