<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/32709?offset=60 https://bioinformaticsonline.com/videolist/watch/19555/a-3d-map-of-the-human-genome Fri, 12 Dec 2014 22:27:55 -0600 https://bioinformaticsonline.com/videolist/watch/19555/a-3d-map-of-the-human-genome <![CDATA[A 3D Map of the Human Genome]]> Suhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist. Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, Erez Lieberman Aiden. (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell.]]> https://bioinformaticsonline.com/researchlabs/view/26569/genome-stability-laboratory Mon, 07 Mar 2016 04:16:32 -0600 <![CDATA[Genome Stability Laboratory]]> The bakers yeast, Saccharomyces cerevisiae is an ideal model organism to understand mechanisms of meiotic chromosome segregation. In S. cerevisiae and in mammals, the majority of meiotic crossovers are formed through a highly conserved MSH4p-MSH5p, MLH1p-MLH3p dependent pathway. We are interested in charactering the role of these complexes in crossover formation and distribution among all homolog pairs. Errors in this process are linked to congenital birth defects in humans such as Down's syndrome.Our laboratory is also interested in understanding the effect of genetic background on mutation rate variation using S. cerevisiae as a model. These studies are relevant for understanding cancer progression, genome evolution and architecture. We use high- throughput genomic methods as well as classical genetics to achieve these aims.

More at http://faculty.iisertvm.ac.in/~nishantkt/index.html

]]> https://bioinformaticsonline.com/researchlabs/view/26499/katju-lab Fri, 26 Feb 2016 03:25:32 -0600 <![CDATA[Katju Lab]]> TheLab seek to understand the genetic factors contributing to genomic variation and phenotypic diversity. To this end, we employ molecular and bioinformatic tools to study evolutionary processes at the level of populations, both experimental and natural, and genomes. Our research interests encompass a wide range of topics, including the evolution of organellar and nuclear genomes, gene duplication and the origin of novel function, and the fitness and phenotypic consequences of mutation in evolution. For details regards ongoing projects, please see the Research page.

http://katjulab.com/research.html

]]> https://bioinformaticsonline.com/bookmarks/view/27427/rcircos-an-r-package-for-circos-2d-track-plots Fri, 20 May 2016 11:01:13 -0500 https://bioinformaticsonline.com/bookmarks/view/27427/rcircos-an-r-package-for-circos-2d-track-plots <![CDATA[RCircos: an R package for Circos 2D track plots]]> RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

]]> Jit https://bioinformaticsonline.com/bookmarks/view/27696/methylkit Fri, 03 Jun 2016 10:09:29 -0500 https://bioinformaticsonline.com/bookmarks/view/27696/methylkit <![CDATA[methylKit]]> methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.

Address of the bookmark: https://github.com/al2na/methylKit

]]> Jit https://bioinformaticsonline.com/bookmarks/view/28269/4dgenome Mon, 04 Jul 2016 00:44:55 -0500 https://bioinformaticsonline.com/bookmarks/view/28269/4dgenome <![CDATA[4DGenome]]> Records in 4DGenome are compiled through comprehensive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted interactions in 5 organisms. Experimental data cover both high throughput datasets and individiual focused studies. 

All interaction data are freely available in a standardized file format. Records can be queried by genomic regions, gene names, organism, and detection technology. 

Address of the bookmark: http://4dgenome.research.chop.edu/

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/36478/the-marvel-assembler Fri, 04 May 2018 19:18:41 -0500 https://bioinformaticsonline.com/bookmarks/view/36478/the-marvel-assembler <![CDATA[The MARVEL assembler]]> MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.

The assembly process can be summarized as follows:

  1. overlap
  2. patch reads
  3. overlap (again)
  4. scrubbing
  5. assembly graph construction and touring
  6. optional read correction
  7. fasta file creation

Address of the bookmark: https://github.com/schloi/MARVEL

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37957/base-a-practical-de-novo-assembler-for-large-genomes-using-long-ngs-reads Fri, 19 Oct 2018 07:25:21 -0500 https://bioinformaticsonline.com/bookmarks/view/37957/base-a-practical-de-novo-assembler-for-large-genomes-using-long-ngs-reads <![CDATA[BASE: a practical de novo assembler for large genomes using long NGS reads]]> new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs.

Address of the bookmark: https://github.com/dhlbh/BASE

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/29235/valet Thu, 22 Sep 2016 04:27:09 -0500 https://bioinformaticsonline.com/bookmarks/view/29235/valet <![CDATA[valet]]>
VALET is a pipeline for performing de novo validation of metagenomic assemblies. VALET checks a number of properties that should hold true for a correct assembly (e.g., mate-pairs are aligned at the correct distance from each other in the assembly, the depth of coverage is fairly uniform along contigs, etc.). The violations of these invariants are reported allowing one to pinpoint areas that were potentially mis-assembled, or to compare the quality of different assemblies. For comparing multiple assemblies of the same data-sets, VALET also reports an overall estimate of the likelihood a particular assembly is correct.
Home Page: 

Address of the bookmark: https://www.cbcb.umd.edu/software/valet

]]> Jit https://bioinformaticsonline.com/bookmarks/view/28842/repeatmodeler Thu, 18 Aug 2016 09:57:15 -0500 https://bioinformaticsonline.com/bookmarks/view/28842/repeatmodeler <![CDATA[RepeatModeler]]> RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.

Address of the bookmark: http://www.repeatmasker.org/RepeatModeler.html

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