<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43319?offset=90 https://bioinformaticsonline.com/bookmarks/view/44182/collection-of-graph-visualization-tools Wed, 25 Jan 2023 02:57:42 -0600 https://bioinformaticsonline.com/bookmarks/view/44182/collection-of-graph-visualization-tools <![CDATA[Collection of Graph Visualization tools !]]> Standard approaches to genome inference and analysis relate sequences to a single linear reference genome. This is efficient but has a fundamental problem: Differences from this reference are hard to observe and describe in a coherent way. Variation and sequence are separated.

image image

https://fungidb.org/fungidb/app/downloads/Current_Release/GultimumBR650/

Address of the bookmark: https://pangenome.github.io/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/30234/last Mon, 19 Dec 2016 14:07:53 -0600 https://bioinformaticsonline.com/bookmarks/view/30234/last <![CDATA[LAST]]> LAST can:

  • Handle big sequence data, e.g:
    • Compare two vertebrate genomes
    • Align billions of DNA reads to a genome
  • Indicate the reliability of each aligned column.
  • Use sequence quality data properly.
  • Compare DNA to proteins, with frameshifts.
  • Compare PSSMs to sequences
  • Calculate the likelihood of chance similarities between random sequences.
  • Do split and spliced alignment.
  • Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

Address of the bookmark: http://last.cbrc.jp/

]]> Bulbul https://bioinformaticsonline.com/bookmarks/view/34493/plast-a-fast-accurate-and-ngs-scalable-bank-to-bank-sequence-similarity-search-tool Fri, 01 Dec 2017 04:10:54 -0600 https://bioinformaticsonline.com/bookmarks/view/34493/plast-a-fast-accurate-and-ngs-scalable-bank-to-bank-sequence-similarity-search-tool <![CDATA[PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool]]> 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/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43877/crowdgo-machine-learning-and-semantic-similarity-guided-consensus-gene-ontology-annotation Thu, 26 May 2022 00:59:49 -0500 https://bioinformaticsonline.com/bookmarks/view/43877/crowdgo-machine-learning-and-semantic-similarity-guided-consensus-gene-ontology-annotation <![CDATA[CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation]]> CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of other tools in order to get an improved precision and recall.

Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It should work on OSX, but please report any errors to maarten.reijnders@unil.ch or create an issue.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010075

Address of the bookmark: https://gitlab.com/mreijnders/crowdgo

]]> Shruti Paniwala https://bioinformaticsonline.com/blog/view/40953/explore-taxdump-files Sat, 08 Feb 2020 04:44:55 -0600 https://bioinformaticsonline.com/blog/view/40953/explore-taxdump-files <![CDATA[Explore taxdump files !]]> 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 ]]> Jit https://bioinformaticsonline.com/bookmarks/view/35907/alienness-rapid-detection-of-candidate-horizontal-gene-transfers-across-the-tree-of-life Mon, 12 Mar 2018 09:24:40 -0500 https://bioinformaticsonline.com/bookmarks/view/35907/alienness-rapid-detection-of-candidate-horizontal-gene-transfers-across-the-tree-of-life <![CDATA[alienness : Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life]]> Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr

http://www.mdpi.com/2073-4425/8/10/248

Address of the bookmark: http://alienness.sophia.inra.fr/cgi/index.cgi

]]> Jit https://bioinformaticsonline.com/researchlabs/view/42327/blaxter-lab Thu, 19 Nov 2020 08:05:28 -0600 <![CDATA[Blaxter Lab]]> Using these high quality genomes we explore

the evolutionary history of genes and species, building phylogenetic trees of life
the contrasting roles of horizontal gene transfer and introgression in shaping evolution
the biology of symbioses, especially symbioses between eukaryotes and bacteria, and between parasites and their hosts
the processes that drive the evolution of pattern in the structure of chromosomes
the diversity of meiofauna, particularly tardigrades, nematodes and other Ecdysozoa
the genomics of extremophilia

More at https://www.sanger.ac.uk/group/blaxter-group/

]]> https://bioinformaticsonline.com/bookmarks/view/36111/d3networktools-for-creating-d3-javascript-network-tree-dendrogram-and-sankey-graphs-from-r Fri, 06 Apr 2018 12:10:45 -0500 https://bioinformaticsonline.com/bookmarks/view/36111/d3networktools-for-creating-d3-javascript-network-tree-dendrogram-and-sankey-graphs-from-r <![CDATA[d3Network:Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.]]> Mike Bostock’s D3.js is great for creating interactive network graphs with JavaScript. The d3Network package makes it easy to create these network graphs from R. The main idea is that you should able to take an R data frame with information about the relationships between members of a network and create full network graphs with one command.

Address of the bookmark: http://christophergandrud.github.io/d3Network/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44157/onezoom-tree-of-life-explorer Sat, 12 Nov 2022 09:29:08 -0600 https://bioinformaticsonline.com/bookmarks/view/44157/onezoom-tree-of-life-explorer <![CDATA[OneZoom tree of life explorer...]]> An interactive map of the evolutionary links between all living things known to science. Discover your favourites, see which species are under threat, and be amazed by the diversity of life on earth.

 

Address of the bookmark: https://www.onezoom.org/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43583/pango-lineage-analysis Mon, 15 Nov 2021 03:38:29 -0600 https://bioinformaticsonline.com/bookmarks/view/43583/pango-lineage-analysis <![CDATA[Pango Lineage Analysis !]]> The Pango nomenclature is being used by researchers and public health agencies worldwide to track the transmission and spread of SARS-CoV-2, including variants of concern. This website documents all current Pango lineages and their spread, as well as various software tools which can be used by researchers to perform analyses on SARS-COV-2 sequence data.

Address of the bookmark: https://cov-lineages.org/resources/pangolin/output.html

]]> Abhi