<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44311?offset=40 https://bioinformaticsonline.com/bookmarks/view/34328/dfast-a-flexible-prokaryotic-genome-annotation-pipeline-for-faster-genome-publication Tue, 14 Nov 2017 10:26:16 -0600 https://bioinformaticsonline.com/bookmarks/view/34328/dfast-a-flexible-prokaryotic-genome-annotation-pipeline-for-faster-genome-publication <![CDATA[DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication]]> We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.

Availability and Implementation

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Address of the bookmark: https://dfast.nig.ac.jp/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39624/cogent-a-tool-for-reconstructing-the-coding-genome-using-high-quality-full-length-transcriptome-sequences Tue, 18 Jun 2019 05:33:04 -0500 https://bioinformaticsonline.com/bookmarks/view/39624/cogent-a-tool-for-reconstructing-the-coding-genome-using-high-quality-full-length-transcriptome-sequences <![CDATA[Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.]]> Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding sequences.
 

Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where there is no reference genome or the ref genome is highly incomplete.

See a recent presentation on Cogent being applied to the Cuttlefish Iso-Seq data.

Cogent preliminary draft paper (updated 2016Dec version), Supplementary

Please see wiki for details on usage.

Address of the bookmark: https://github.com/Magdoll/Cogent

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases Wed, 12 Feb 2020 01:16:29 -0600 https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases <![CDATA[Biological databases !]]> Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/30304/mcscan Thu, 22 Dec 2016 03:53:58 -0600 https://bioinformaticsonline.com/bookmarks/view/30304/mcscan <![CDATA[MCscan]]> MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences in Plant Genome Duplication Database. It is intended as an easy-to-use and quick way to identify conserved gene arrays both within the same genome and across different genomes.

More at http://chibba.agtec.uga.edu/duplication/mcscan/

Address of the bookmark: http://chibba.agtec.uga.edu/duplication/mcscan/

]]> Bulbul https://bioinformaticsonline.com/bookmarks/view/30550/genomering-alignment-visualization-based-on-supergenome-coordinates Wed, 18 Jan 2017 10:24:10 -0600 https://bioinformaticsonline.com/bookmarks/view/30550/genomering-alignment-visualization-based-on-supergenome-coordinates <![CDATA[GenomeRing: alignment visualization based on SuperGenome coordinates]]> The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. Computational tools that can visualize genome alignments in a meaningful manner are needed to help researchers gain new insights into the underlying data. Such visualizations typically are either realized in a linear fashion as in genome browsers or by using a circular approach, where relationships between genomic regions are indicated by arcs. Both methods allow for the integration of additional information such as experimental data or annotations. However, providing a visualization that still allows for a quick and comprehensive interpretation of all important genomic variations together with various supplemental data, which may be highly heterogeneous, remains a challenge.

More at https://academic.oup.com/bioinformatics/article/28/12/i7/268598/GenomeRing-alignment-visualization-based-on

Address of the bookmark: http://it.informatik.uni-tuebingen.de/?page_id=185

]]> Neel https://bioinformaticsonline.com/bookmarks/view/43888/syri-compares-alignments-between-two-chromosome-level-assemblies-and-identifies-synteny-and-structural-rearrangements Wed, 01 Jun 2022 02:01:13 -0500 https://bioinformaticsonline.com/bookmarks/view/43888/syri-compares-alignments-between-two-chromosome-level-assemblies-and-identifies-synteny-and-structural-rearrangements <![CDATA[Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.]]> Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.

image

Address of the bookmark: https://github.com/schneebergerlab/syri

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/26559/microscope Fri, 04 Mar 2016 05:26:31 -0600 https://bioinformaticsonline.com/bookmarks/view/26559/microscope <![CDATA[Microscope]]> Microscope Platform user documentation.

The MicroScope platform is available at this URL:

https://www.genoscope.cns.fr/agc/microscope

Address of the bookmark: http://microscope.readthedocs.org/en/latest/index.html

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/42661/3d-genome-browser-explore-chromatin-interaction-data-such-as-hi-c-chia-pet-capture-hi-c-plac-seq-and-more Fri, 22 Jan 2021 20:19:32 -0600 https://bioinformaticsonline.com/bookmarks/view/42661/3d-genome-browser-explore-chromatin-interaction-data-such-as-hi-c-chia-pet-capture-hi-c-plac-seq-and-more <![CDATA[3D Genome Browser: explore chromatin interaction data, such as Hi-C, ChIA-PET, Capture Hi-C, PLAC-Seq, and more]]> Beside visualizing chromatin interaction data, you can also seamlessly browse other omics data such as ChIP-Seq or RNA-Seq for the same genomic region, and gain a complete view of both regulatory landscape and 3D genome structure for any given gene. You can also check the expression of any queried gene across hundreds of tissue/cell types measured by the ENCODE consortium. Finally, please check out the virtual 4C page, where we provide multiple methods to link distal cis-regulatory elements with their potential target genes, including virtual 4C, ChIA-PET and cross-cell-type correlation of proximal and distal DHSs.

Address of the bookmark: http://3dgenome.fsm.northwestern.edu/index.html

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/33960/mgra-breakpoint-graphs-and-ancestral-genome-reconstructions Tue, 25 Jul 2017 08:48:25 -0500 https://bioinformaticsonline.com/bookmarks/view/33960/mgra-breakpoint-graphs-and-ancestral-genome-reconstructions <![CDATA[MGRA: Breakpoint graphs and ancestral genome reconstructions]]> MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and evolutionary history of extant genomes.

It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and produces such sequences for ancestral genomes at the internal nodes of the phylogenetic tree.

The phylogenetic tree may be also specified completely or partially, in the latter case MGRA can reconstruct conserved ancestral regions (CARs) of the ancestral genome of interest.

Since version 2 MGRA supports gene insertion and deletions in addition to genome rearrangements and allows the input genomes to have different gene content.

It also can reconstruct most plausible phylogenetic tree based on the rearrangement characters.

Address of the bookmark: http://mgra.cblab.org/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34413/coursera-genome-assembly-tutorial Sat, 25 Nov 2017 08:57:25 -0600 https://bioinformaticsonline.com/bookmarks/view/34413/coursera-genome-assembly-tutorial <![CDATA[coursera genome assembly tutorial]]> Solutions to Coursera Genome Sequencing (Bioinformatics II)

Address of the bookmark: https://github.com/iansealy/coursera-assembly

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