<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44902?offset=340 https://bioinformaticsonline.com/bookmarks/view/33691/annotationsketch Sun, 25 Jun 2017 17:54:22 -0500 https://bioinformaticsonline.com/bookmarks/view/33691/annotationsketch <![CDATA[AnnotationSketch]]> The AnnotationSketch module is a versatile and efficient C-based drawing library for GFF3-compatible genomic annotations. It is included in the GenomeTools distribution. Additionally, bindings to the Lua, Python and Rubyprogramming languages are provided.

http://genometools.org/annotationsketch.html

Address of the bookmark: http://genometools.org/annotationsketch.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39869/mfannot-a-program-for-the-annotation-of-mitochondrial-and-plastid-genomes Mon, 26 Aug 2019 11:47:56 -0500 https://bioinformaticsonline.com/bookmarks/view/39869/mfannot-a-program-for-the-annotation-of-mitochondrial-and-plastid-genomes <![CDATA[MFannot : a program for the annotation of mitochondrial and plastid genomes]]> MFannot is a program for the annotation of mitochondrial and plastid genomes

MFannot is a program for the annotation of mitochondrial and plastid genomes. It is a PERL wrapper around a set of diverse, external independent tools.

It makes intense use of RNA/intron detection tools including HMMER, Exonerate, Erpin and others.

http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl

Address of the bookmark: https://github.com/BFL-lab/Mfannot

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41602/nucdiff-in-depth-characterization-and-annotation-of-differences-between-two-sets-of-dna-sequences Tue, 05 May 2020 10:35:48 -0500 https://bioinformaticsonline.com/bookmarks/view/41602/nucdiff-in-depth-characterization-and-annotation-of-differences-between-two-sets-of-dna-sequences <![CDATA[NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences]]> NucDiff locates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements and various local differences. These features make NucDiff to be perfectly suitable to compare assemblies with each other or with available reference genomes.

NucDiff provides information about the types of differences and their locations. It is possible to upload the results into genome browser for visualization and further inspection. It was written in Python and uses the NUCmer package from MUMmer[1] for sequence comparison.



Address of the bookmark: https://github.com/uio-cels/NucDiff

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43062/jcvi-utility-libraries Sat, 08 May 2021 22:04:02 -0500 https://bioinformaticsonline.com/bookmarks/view/43062/jcvi-utility-libraries <![CDATA[JCVI utility libraries]]> Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

Address of the bookmark: https://github.com/tanghaibao/jcvi

]]> Jit https://bioinformaticsonline.com/bookmarks/view/33219/dbcan-a-web-server-and-database-for-automated-carbohydrate-active-enzyme-annotation Mon, 29 May 2017 05:39:29 -0500 https://bioinformaticsonline.com/bookmarks/view/33219/dbcan-a-web-server-and-database-for-automated-carbohydrate-active-enzyme-annotation <![CDATA[dbCAN: a web server and DataBase for automated Carbohydrate-active enzyme ANnotation]]> dbCAN is a web server and DataBase for automated Carbohydrate-active enzyme ANnotation, funded by the BioEnergy Science Center of the DOE. Similar resources on the web include CAZy database and CAT. All data in dbCAN are generated based on the family classification from CAZy database while it has the following unique features compared with CAZy database and CAT:

  • dbCAN provides the capability of automated and comprehensive CAZyme annotation of a given genome submitted by the user;
  • dbCAN provides an explicitly defined signature domain for each and every CAZyme family along with its location in all the relevant full-length CAZyme proteins in all sequenced genomes;
  • dbCAN provides the most complete set of metagenomic CAZyme genes published so far and represents the first step towards discovering novel CAZyme catalysts in metagenomes;
  • dbCAN provides a subfamily classification of the existing CAZyme families based on sequence similarities;
  • dbCAN make all pre-computed data freely available to the public, including sequence alignments, hidden markov models (HMMs) and phylogenies of the signature domain regions in each and every CAZyme family and subfamily.

dbCAN is updated regularly when CAZy database created new families based on latest literature.

Address of the bookmark: http://csbl.bmb.uga.edu/dbCAN/index.php

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37550/mirem-an-expectation-maximization-approach-for-prioritizing-mirnas-associated-with-gene-set Thu, 16 Aug 2018 04:48:07 -0500 https://bioinformaticsonline.com/bookmarks/view/37550/mirem-an-expectation-maximization-approach-for-prioritizing-mirnas-associated-with-gene-set <![CDATA[miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set]]> From list of genes... ... to microRNAs

Using established miRNA-interaction databases, miREM combines hypergeometric and expectation-maximization algorithms to sieve through your genetic data for microRNA signatures

https://bioinfo-csi.nus.edu.sg/mirem2/

Address of the bookmark: https://bioinfo-csi.nus.edu.sg/mirem2/

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/44513/mike-an-ultrafast-assembly-and-alignment-free-approach-for-phylogenetic-tree-construction Mon, 08 Apr 2024 06:19:52 -0500 https://bioinformaticsonline.com/bookmarks/view/44513/mike-an-ultrafast-assembly-and-alignment-free-approach-for-phylogenetic-tree-construction <![CDATA[MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction]]> MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction.

Address of the bookmark: https://github.com/Argonum-Clever2/mike

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/33003/surankco-supervised-ranking-of-contigs-in-de-novo-assemblies Wed, 24 May 2017 04:46:52 -0500 https://bioinformaticsonline.com/bookmarks/view/33003/surankco-supervised-ranking-of-contigs-in-de-novo-assemblies <![CDATA[SuRankCo: supervised ranking of contigs in de novo assemblies]]> SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0644-7

 

Address of the bookmark: https://sourceforge.net/projects/surankco/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/37737/rebaler-program-for-conducting-reference-based-assemblies-using-long-reads Tue, 18 Sep 2018 07:52:41 -0500 https://bioinformaticsonline.com/bookmarks/view/37737/rebaler-program-for-conducting-reference-based-assemblies-using-long-reads <![CDATA[Rebaler: program for conducting reference-based assemblies using long reads.]]> Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences.

I made Rebaler for bacterial genomes (specifically for the task of testing basecallers). It should in principle work for non-bacterial genomes as well, but I haven't tested it.

Address of the bookmark: https://github.com/rrwick/Rebaler

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40359/minipolish-a-tool-for-racon-polishing-of-miniasm-assemblies Tue, 03 Dec 2019 02:40:54 -0600 https://bioinformaticsonline.com/bookmarks/view/40359/minipolish-a-tool-for-racon-polishing-of-miniasm-assemblies <![CDATA[Minipolish: A tool for Racon polishing of miniasm assemblies]]> Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long reads.

Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs that miniasm makes.

That's where Minipolish comes in. With a single command, it will use Racon to polish up a miniasm assembly, while keeping the assembly in graph form.

It also takes care of some of the other nuances of polishing a miniasm assembly:

  • Adding read depth information to contigs
  • Fixing sequence truncation that can occur in Racon
  • Adding circularising links to circular contigs if not already present (so they display better in Bandage)
  • 'Rotating' circular contigs between polishing rounds to ensure clean circularisation

Address of the bookmark: https://github.com/rrwick/Minipolish

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