BOL: Related items

GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks

Rahul Nayak — Tue, 15 Jan 2019 09:39:30 -0600

GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks based on gene expression data and optional hub gene information.

It efficiently constructs gene networks from expression data. It allows the user to use ten different network construction methods (such as partial correlation-, likelihood-, Bayesian- and mutual information-based methods) and integrates the resulting networks from multiple methods. Hub gene information, if available, can be incorporated to enhance performance.

GeNeCK is an efficient and easy-to-use web application for gene regulatory network construction. It can be accessed at http://lce.biohpc.swmed.edu/geneck

Address of the bookmark: http://lce.biohpc.swmed.edu/geneck/

PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes

BioStar — Thu, 13 Aug 2020 10:06:19 -0500

PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends on performing a all-vs-all sequence comparison, usually using BLAST, to determine homology. However, these methods are computationally expensive, requiring O(n2) resources to identify RBHs. This is problematic, as the modern deluge of sequencing data means that comparative genomics analyses could be performed on datasets of thousands of strains.

Address of the bookmark: https://github.com/ryanmelnyk/PyParanoid

homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

Abhi — Sat, 03 Jun 2023 19:19:10 -0500

This tutorial describes the usage of homologizer to phase gene copies into polyploid subgenomes. The tutorial is an abbreviated version of a soon-to-be published paper in Methods in Molecular Biology. Please see that paper for many more details and practical considerations for running homologizer analyses. If you use homologizer, please cite the paper in which we first describe the method:

Freyman, W.A., Johnson, M.G., and C.J. Rothfels. 2022. Homologizer: phylogenetic phasing of gene copies into polyploid subgenomes. bioRxiv 2020.10.22.351486v4

homologizer is implemented in RevBayes. Please see http://revbayes.com to download and install RevBayes. For users without previous RevBayes experience, we recommend the tutorials at http://revbayes.com.

Address of the bookmark: https://github.com/wf8/homologizer

Explore taxdump files !

Jit — Sat, 08 Feb 2020 04:44:55 -0600

This is an extract of taxdump-readme.txt to be found at 
ftp://ftp.ncbi.nih.gov/pub/taxonomy/

The content of the archive
--------------------------

It may look like this:

delnodes.dmp
division.dmp
gencode.dmp
merged.dmp
names.dmp
nodes.dmp
readme.txt

The readme.txt file gives a brief description of *.dmp files. These files
contain taxonomic information and are briefly described below. Each of the
files store one record in the single line that are delimited by "\t|\n"
(tab, vertical bar, and newline) characters. Each record consists of one 
or more fields delimited by "\t|\t" (tab, vertical bar, and tab) characters.
The brief description of field position and meaning for each file follows.

nodes.dmp
---------

This file represents taxonomy nodes. The description for each node includes 
the following fields:

	tax_id					-- node id in GenBank taxonomy database
 	parent tax_id				-- parent node id in GenBank taxonomy database
 	rank					-- rank of this node (superkingdom, kingdom, ...) 
 	embl code				-- locus-name prefix; not unique
 	division id				-- see division.dmp file
 	inherited div flag  (1 or 0)		-- 1 if node inherits division from parent
 	genetic code id				-- see gencode.dmp file
 	inherited GC  flag  (1 or 0)		-- 1 if node inherits genetic code from parent
 	mitochondrial genetic code id		-- see gencode.dmp file
 	inherited MGC flag  (1 or 0)		-- 1 if node inherits mitochondrial gencode from parent
 	GenBank hidden flag (1 or 0)            -- 1 if name is suppressed in GenBank entry lineage
 	hidden subtree root flag (1 or 0)       -- 1 if this subtree has no sequence data yet
 	comments				-- free-text comments and citations

names.dmp
---------
Taxonomy names file has these fields:

	tax_id					-- the id of node associated with this name
	name_txt				-- name itself
	unique name				-- the unique variant of this name if name not unique
	name class				-- (synonym, common name, ...)

division.dmp
------------
Divisions file has these fields:
	division id				-- taxonomy database division id
	division cde				-- GenBank division code (three characters)
	division name				-- e.g. BCT, PLN, VRT, MAM, PRI...
	comments

gencode.dmp
-----------
Genetic codes file:

	genetic code id				-- GenBank genetic code id
	abbreviation				-- genetic code name abbreviation
	name					-- genetic code name
	cde					-- translation table for this genetic code
	starts					-- start codons for this genetic code

delnodes.dmp
------------
Deleted nodes (nodes that existed but were deleted) file field:

	tax_id					-- deleted node id

merged.dmp
----------
Merged nodes file fields:

	old_tax_id                              -- id of nodes which has been merged
	new_tax_id                              -- id of nodes which is result of merging

PubMed opens for comment

Rahul Nayak — Thu, 24 Oct 2013 12:40:17 -0500

The informal conversations that researchers have at scientific meetings look set to move online, if a new initiative by the US National Center for Biotechnology Information (NCBI) has its way. On 22 October, the NCBI of Bethesda, Maryland, launched the pilot phase of a programme called PubMed Commons. This will allow users to comment on published abstracts on the PubMed website, which indexes some 22 million papers.

For now, only a select group of researchers and their invited guests can use the system. But the NCBI's director David Lipman, who helped to develop the programme, says that soon any PubMed author will be allowed to comment under his or her real name and anyone will be able to read the comments.

More @ http://www.nature.com/news/pubmed-opens-for-comment-1.14023

News source Nature.

NCBI Remap

Jit — Thu, 11 Feb 2016 11:02:26 -0600

NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use the API for NCBI Remap.

More at http://www.ncbi.nlm.nih.gov/genome/tools/remap

API http://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/api

Address of the bookmark: http://www.ncbi.nlm.nih.gov/genome/tools/remap

MutaBind

Jit — Mon, 06 Jun 2016 13:34:09 -0500

MutaBind is a new computational method and server created through NCBI research efforts that maps mutations on a protein structural complex, calculates changes in binding affinity, identifies deleterious mutations and produces a downloadable mutant structural model. http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

MutaBind guides you through this process, step by step, starting with selecting a protein complex and inputting PDB code or uploading PDB files. You can also retrieve results with a job ID number, view help documents, and review the MutaBind method and references.

More at http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

NCBI Prokaryotic Genome Annotation Pipeline

Jit — Tue, 16 May 2017 08:56:03 -0500

NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume. You can find a more detailed description of the new version of the pipeline in NCBI Handbook chapter. NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

https://www.ncbi.nlm.nih.gov/genome/annotation_prok/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/

BLAST nr version 5 database, (nr_v5)

Jit — Fri, 23 Aug 2019 11:35:35 -0500

NCBI have made changes the nr version 5 database, (nr_v5), to facilitate better search results and improved performance by reducing the number of redundant titles in the nr_v5 database used by webBLAST, which is also available for BLAST+ users.

The changes in nr preserve the taxonomic diversity of the entries in the database while reducing the number of titles for identical sequences. GenPept accessions are still accessible via www.ncbi.nlm.nih.gov/protein/$GENBANK_ACCESSION or the IPG website https://www.ncbi.nlm.nih.gov/ipg/.

The "Identical Proteins" link in the alignments section of the webBLAST results takes you to a full list of all accessions associated with a sequence.

For BLAST+ users downloading nr_v5: the database is now approximately 50% smaller, resulting in faster downloads and BLAST searches, and smaller disk space requirements. The database is downloadable at: ftp://ftp.ncbi.nlm.nih.gov/blast/db/v5/

For BLAST+ there is a cleanup script to help you manage the transition to this smaller database. The script removes unused database volumes: ftp://ftp.ncbi.nlm.nih.gov/blast/temp/cleanup-blastdb-volumes.py

Here are the new rules on how we keep titles in nr_v5:

1. We keep all refseq, swissprot, pir and PDB titles.

2. We keep any GenPept titles with a TAXID that has not already been seen in the record.

3. We keep at least five GenPept titles regardless of whether the TAXIDS have been seen before or not in this record.

NCBI BLAST have added new columns to the Descriptions

Neel — Tue, 01 Dec 2020 09:56:07 -0600

NCBI BLAST have added new columns to the Descriptions Table for web BLAST output. The new columns are Scientific Name, Common Name, Taxid, and Accession Length. Common Name and Accession Length are now part of the default display. You can click 'Select columns' or 'Manage columns' to add or remove columns from the display Your preferences will be saved for your next visit to BLAST, and when you download your results, whatever columns you have displayed will be saved. See the NCBI Insights post (https://go.usa.gov/x7fPE) for more details.