<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/33955?offset=20 https://bioinformaticsonline.com/bookmarks/view/37257/asar-advanced-metagenomic-sequence-analysis-in-r Mon, 09 Jul 2018 05:20:50 -0500 https://bioinformaticsonline.com/bookmarks/view/37257/asar-advanced-metagenomic-sequence-analysis-in-r <![CDATA[ASAR: Advanced metagenomic Sequence Analysis in R]]> An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

Address of the bookmark: https://github.com/Askarbek-orakov/ASAR

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41689/medaka-sequence-correction-provided-by-ont-research Mon, 18 May 2020 16:28:00 -0500 https://bioinformaticsonline.com/bookmarks/view/41689/medaka-sequence-correction-provided-by-ont-research <![CDATA[medaka: Sequence correction provided by ONT Research]]> medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.

Address of the bookmark: https://github.com/nanoporetech/medaka

]]> BioStar https://bioinformaticsonline.com/blog/view/43995/tools-for-sequence-translation Tue, 08 Nov 2022 03:37:58 -0600 https://bioinformaticsonline.com/blog/view/43995/tools-for-sequence-translation <![CDATA[Tools for Sequence translation !]]> BOrf - https://github.com/betsig/borf

CodAn - https://github.com/pedronachtigall/CodAn

EMBOSS-Sixpack - https://www.ebi.ac.uk/Tools/st/emboss_sixpack/

esl-translate - http://hmmer.org/, https://github.com/EddyRivasLab/easel

GeneMarkS-T - http://exon.gatech.edu/GeneMark/license_download.cgi

ORFfinder - https://www.ncbi.nlm.nih.gov/orffinder/ (web server)

PLASS - https://github.com/soedinglab/plass

Prodigal - https://github.com/hyattpd/Prodigal

TransDecoder - https://github.com/TransDecoder/TransDecoder

]]> Abhi https://bioinformaticsonline.com/fun/view/4196/chemical-elements-of-bioinformatics Tue, 03 Sep 2013 16:35:39 -0500 https://bioinformaticsonline.com/fun/view/4196/chemical-elements-of-bioinformatics <![CDATA[Chemical Elements of Bioinformatics]]> You must be familiar with periodic table and colour pattern, but this time you are going to amaze by new elements table by Eagle genomics. Just check it out and have fun :)

http://elements.eaglegenomics.com/

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/34391/taxoblast-taxoblast-is-a-pipeline-to-identify-contamination-in-genomic-sequence Thu, 23 Nov 2017 08:37:15 -0600 https://bioinformaticsonline.com/bookmarks/view/34391/taxoblast-taxoblast-is-a-pipeline-to-identify-contamination-in-genomic-sequence <![CDATA[Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence]]> Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast).

Address of the bookmark: https://sourceforge.net/projects/taxoblast/files/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35550/circoletto-visualizing-sequence-similarity-with-circos Fri, 09 Feb 2018 10:23:40 -0600 https://bioinformaticsonline.com/bookmarks/view/35550/circoletto-visualizing-sequence-similarity-with-circos <![CDATA[Circoletto: visualizing sequence similarity with Circos]]> Circoletto, an online visualization tool based on Circos, which provides a fast, aesthetically pleasing and informative overview of sequence similarity search results.

Online version and downloadable software package for offline use (source code in PERL) freely available at http://bat.ina.certh.gr/tools/circoletto/

Contact:ndarz@certh.gr

Address of the bookmark: http://tools.bat.infspire.org/circoletto/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39098/sda-long-read-sequence-and-assembly-of-segmental-duplications Tue, 05 Mar 2019 10:00:57 -0600 https://bioinformaticsonline.com/bookmarks/view/39098/sda-long-read-sequence-and-assembly-of-segmental-duplications <![CDATA[SDA: Long-read sequence and assembly of segmental duplications]]> Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct paralogs.

https://github.com/mvollger/SDA

Address of the bookmark: https://www.nature.com/articles/s41592-018-0236-3

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39881/apollo-a-sequence-annotation-editor Tue, 27 Aug 2019 08:08:47 -0500 https://bioinformaticsonline.com/bookmarks/view/39881/apollo-a-sequence-annotation-editor <![CDATA[Apollo: a sequence annotation editor]]> The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them

Address of the bookmark: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2002-3-12-research0082

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/40814/accesssyri-finding-genomic-rearrangements-and-local-sequence-differences-from-whole-genome-assemblies Sat, 01 Feb 2020 13:38:49 -0600 https://bioinformaticsonline.com/bookmarks/view/40814/accesssyri-finding-genomic-rearrangements-and-local-sequence-differences-from-whole-genome-assemblies <![CDATA[AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies]]> AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies

SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1911-0

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

]]> Jit https://bioinformaticsonline.com/news/view/41562/submit-your-sars-cov-2-sequence-data-to-genbank Thu, 09 Apr 2020 18:28:25 -0500 https://bioinformaticsonline.com/news/view/41562/submit-your-sars-cov-2-sequence-data-to-genbank <![CDATA[Submit your SARS-CoV-2 sequence data to GenBank]]> Submit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page. Submission is simple and streamlined *and* there’s a rapid turnaround. https://submit.ncbi.nlm.nih.gov/sarscov2/
 
Quickly and easily add your SARS-CoV-2 sequence data to the growing public archive with new, special features and support from NCBI. new SARS-CoV-2 sequence submission landing page will help you get started. GenBank submissions are accessioned and released in approximately 1-2 working days, and Sequence Read Archive (SRA) submissions typically processed and released within hours. Submission is simple!
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