BOL: Related items

TACOA: Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

Poonam Mahapatra — Tue, 15 May 2018 09:52:28 -0500

TACOA is a software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function. TACOA can be easily installed and run on a desktop computer, therefore allowing researchers to locally analyze their metagenomic sequence data or integrate it into their pipelines.

Address of the bookmark: http://www.cebitec.uni-bielefeld.de/index.php/2-uncategorised/99-tacoa

k-mers tutorial - classification and taxonomy

Neel — Thu, 26 Aug 2021 10:28:43 -0500

DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently, discard redundant data, and count them efficiently.

More recently, we've been enthused about using k-mer based similarity measures and computing and searching k-mer-based sketch search databases for all the things.

But I haven't spent too much talking about using k-mers for taxonomy, although that has become an ahem area of interest recently, if you read into our papers a bit.

In this blog post I'm going to fix this by doing a little bit of a literature review and waxing enthusiastic about other people's work. Then in a future blog post I'll talk about how we're building off of this work in fun! and interesting? ways!

Address of the bookmark: http://ivory.idyll.org/blog/2017-something-about-kmers.html

Tools for RNA classification

Abhi — Tue, 08 Nov 2022 03:39:11 -0600

barrnap - https://github.com/tseemann/barrnap

CPAT - https://github.com/liguowang/cpat, http://lilab.research.bcm.edu/ (web server)

CPC2 - https://github.com/gao-lab/CPC2_standalone, http://cpc2.gao-lab.org/ (web server)

Infernal - http://eddylab.org/infernal/, https://github.com/EddyRivasLab/infernal

NCBI RefSeq - https://www.ncbi.nlm.nih.gov/refseq/

Rfam - http://rfam.xfam.org/, https://docs.rfam.org/en/latest/index.html

SILVA - https://www.arb-silva.de/

RNAmmer - http://www.cbs.dtu.dk/services/RNAmmer/ (web server, standalone download link)

Pangolin tutorial !

Abhi — Fri, 10 Dec 2021 05:58:59 -0600

This is a tutorial for using the Pangolin Web Application. For information on using the command line tool, please visit the command line tool usage page.

https://cov-lineages.org/resources/pangolin/tutorial.html

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

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Poonam Mahapatra — Mon, 04 Jun 2018 03:45:15 -0500

One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies, including LTR-retrotransposon Retrieve corresponding TE sequences, and flanking sequences, from the local fasta files Compute summary statistics for each TE family (number of TE copies, genome coverage...) Ambiguous cases such as nested TE can be assembled into copies automatically or manually Allow for working with a TE user-defined library Allow for working with only a user-chosen set of TE families http://doua.prabi.fr/software/one-code-to-find-them-all

Address of the bookmark: http://doua.prabi.fr/software/one-code-to-find-them-all