<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36398?offset=120 https://bioinformaticsonline.com/bookmarks/view/41996/wgd%E2%80%94simple-command-line-tools-for-the-analysis-of-ancient-whole-genome-duplications Thu, 23 Jul 2020 05:49:45 -0500 https://bioinformaticsonline.com/bookmarks/view/41996/wgd%E2%80%94simple-command-line-tools-for-the-analysis-of-ancient-whole-genome-duplications <![CDATA[wgd—simple command line tools for the analysis of ancient whole-genome duplications]]> wgd is a easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.

https://academic.oup.com/bioinformatics/article/35/12/2153/5162749

Address of the bookmark: https://github.com/arzwa/wgd

]]> LEGE https://bioinformaticsonline.com/blog/view/43084/frequently-used-bioinformatics-tools-for-viral-genome-analysis Wed, 23 Jun 2021 07:40:41 -0500 https://bioinformaticsonline.com/blog/view/43084/frequently-used-bioinformatics-tools-for-viral-genome-analysis <![CDATA[Frequently used bioinformatics tools for viral genome analysis !]]> IVA: accurate de novo assembly of RNA virus genomes.
Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD.
Bioinformatics. 2015 Jul 15;31(14):2374-6. doi: 10.1093/bioinformatics/btv120. Epub 2015 Feb 28.

Adapter sequences:
Optimal enzymes for amplifying sequencing libraries.
Quail, M. a et al. Nat. Methods 9, 10-1 (2012).

GAGE:
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Salzberg, S. L. et al. Genome Res. 22, 557-67 (2012).

KMC:
Disk-based k-mer counting on a PC.
Deorowicz, S., Debudaj-Grabysz, A. & Grabowski, S. BMC Bioinformatics 14, 160 (2013).

Kraken:
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood, D. E. & Salzberg, S. L. Genome Biol. 15, R46 (2014).

MUMmer:
Versatile and open software for comparing large genomes.
Kurtz, S. et al. Genome Biol. 5, R12 (2004).

R:
R: A language and environment for statistical computing.
R Core Team (2013). R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.

RATT:
RATT: Rapid Annotation Transfer Tool.
Otto, T. D., Dillon, G. P., Degrave, W. S. & Berriman, M. Nucleic Acids Res. 39, e57 (2011).

SAMtools:
The Sequence Alignment/Map format and SAMtools.
Li, H. et al. Bioinformatics 25, 2078-9 (2009).

Trimmomatic:
Trimmomatic: A flexible trimmer for Illumina Sequence Data.
Bolger, A. M., Lohse, M. & Usadel, B. Bioinformatics 1-7 (2014).

]]> Neel https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools Thu, 17 Feb 2022 05:37:55 -0600 https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools <![CDATA[Comparative genomics visualisation tools !]]> Comparative genomics visualisation tools !

Address of the bookmark: https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&selected=%23BRIG&tag=Comparative

]]> Neel https://bioinformaticsonline.com/blog/view/44551/bioinformatic-tools-for-pathogens-informatics-at-cvr Sat, 08 Jun 2024 15:59:46 -0500 https://bioinformaticsonline.com/blog/view/44551/bioinformatic-tools-for-pathogens-informatics-at-cvr <![CDATA[Bioinformatic tools for pathogens informatics at CVR]]>

Novel sequencing and analytical approaches focused on studying viruses and virus-host interactions. Below you will find summaries and links to a number of bioinformatic tools that have been developed @ CVR.

The database-integrated genome-screening (DIGS) tool provides a framework for implementing automated in silico screening of sequence databases using BLAST in combination with a relational database (MySQL).

DisCVR is a Diagnostic tool for detecting known human viruses in clinical samples from Next-Generation Sequencing (NGS) data. The tool uses a simple and straightforward Graphical User Interface and is optimized on Windows OS without compromising speed and accuracy.

DiversiTools is a computational tool that is specifically tailored towards viral HTS data sets and the analysis of the underlying viral populations that they represent. It was initially developed in collaboration with a number of virologists interested in characterising the intra-host diversity of viral populations and studying their evolution across transmission chains at the micro-evolutionary scale.

GLUE is a flexible data-centric bioinformatics environment for virus sequence data, with a focus on virus evolution and genomic variation. GLUE has been applied to a range of viruses. A GLUE-based resource focused on Hepatitis C virus is HCV-GLUE.

Tanoti is a BLAST guided reference based short read aligner. It is developed for maximising alignment in highly variable next generation sequence data sets (Illumina).

ViCTree is a bioinformatic framework that automatically selects new candidate virus sequences from GenBank, generates multiple sequence alignments, calculates a maximum likelihood phylogeny and integrates the sequences into the existing phylogenetic trees. For more information click here.

Viral Host Predictor provides a fast and simple way to predict the hosts and vectors of RNA viruses from viral sequences.

GRACy is a bioinformatic tool designed for the analysis of Illumina data originated from Human cytomegalovirus samples. GRACy can be used to perform read quality filtering, genotyping, de novo assembly, variant detection, annotation and data submission to public database.

LoReTTA (Long Read Template Targeted Assembler) is a reference assisted de novo assembler specifically designed to deal with PacBio reads generated from viral genomes. 

BingleSeq is a R-package enables the user-friendly analysis of count tables obtained by both Bulk RNA-Seq and single-cell RNA-Seq protocols. The development of BingleSeq focused on providing a flexible and intuitive user experience.

]]> Abhi https://bioinformaticsonline.com/blog/view/20328/research-article-publiaction Fri, 09 Jan 2015 18:50:17 -0600 https://bioinformaticsonline.com/blog/view/20328/research-article-publiaction <![CDATA[Research article- Publiaction]]> Dear All,

I am Lalit, Working as SRF In Haffkine Institute. I would like to publish research article related to protein modeling and docking which in cludes MD as final step.

I am currently working on protein modeling and docking area. 

Those who are interested . Kindly contact me on this email id:samantlalit@gmail.com

]]> LALIT SAMANT https://bioinformaticsonline.com/bookmarks/view/27479/biogps Mon, 23 May 2016 03:15:46 -0500 https://bioinformaticsonline.com/bookmarks/view/27479/biogps <![CDATA[BioGPS]]> A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.

http://biogps.org/#goto=welcome

Address of the bookmark: http://biogps.org/#goto=welcome

]]> Anjana https://bioinformaticsonline.com/bookmarks/view/33651/darkhorse-a-method-for-genome-wide-prediction-of-horizontal-gene-transfer Thu, 22 Jun 2017 07:58:35 -0500 https://bioinformaticsonline.com/bookmarks/view/33651/darkhorse-a-method-for-genome-wide-prediction-of-horizontal-gene-transfer <![CDATA[DarkHorse: a method for genome-wide prediction of horizontal gene transfer]]> A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. The method is also useful for retrospective assessments of horizontal transfer prediction reliability, recognizing orthologous sequences that may have been previously overlooked or unavailable. These features are demonstrated in bacterial, archaeal, and eukaryotic examples.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852411/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36849/glean-an-unsupervised-learning-system-to-integrate-disparate-sources-of-gene-structure-evidence Sat, 02 Jun 2018 07:38:33 -0500 https://bioinformaticsonline.com/bookmarks/view/36849/glean-an-unsupervised-learning-system-to-integrate-disparate-sources-of-gene-structure-evidence <![CDATA[GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence]]> GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.

Address of the bookmark: https://sourceforge.net/projects/glean-gene/

]]> Poonam Mahapatra https://bioinformaticsonline.com/bookmarks/view/4943/molecular-genetics-lecture Fri, 27 Sep 2013 04:24:45 -0500 https://bioinformaticsonline.com/bookmarks/view/4943/molecular-genetics-lecture <![CDATA[Molecular Genetics Lecture]]> "Robert Sapolsky makes interdisciplinary connections between behavioral biology and molecular genetic influences. He relates protein synthesis and point mutations to microevolutionary change, and discusses conflicting theories of gradualism and punctuated equilibrium and the influence of epigenetics on development theories." 

"Robert Sapolsky is an American neuroendocrinologist, professor of biology, neuroscience, and neurosurgery at Stanford University, researcher and author" ----Wikipedia

Address of the bookmark: http://www.youtube.com/watch?v=_dRXA1_e30o

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/36752/minmax-a-versatile-tool-for-calculating-and-comparing-synonymous-codon-usage-and-its-impact-on-protein-folding Thu, 24 May 2018 02:53:31 -0500 https://bioinformaticsonline.com/bookmarks/view/36752/minmax-a-versatile-tool-for-calculating-and-comparing-synonymous-codon-usage-and-its-impact-on-protein-folding <![CDATA[%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding.]]> Address of the bookmark: http://www.codons.org/

]]> Surabhi Chaudhary