<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/41804?offset=90 https://bioinformaticsonline.com/videolist/watch/4961/genetics-epigenetics-and-disease Fri, 27 Sep 2013 11:32:55 -0500 https://bioinformaticsonline.com/videolist/watch/4961/genetics-epigenetics-and-disease <![CDATA[Genetics, epigenetics and disease]]> Royal Society GlaxoSmithKline Prize Lecture given by Professor Adrian Bird CBE FMedSci FRS on Tuesday 22 January 2013. Adrian Bird CBE FMedSci FRS is the Buchanan Chair of Genetics at the University of Edinburgh. The human genome sequence has been available for more than a decade, but its significance is still not fully understood. While most human genes have been identified, there is much to learn about the DNA signals that control them. This lecture described an unusually short DNA sequence, just two base pairs long, CG, which occurs in several chemically different forms. Defects in signalling by CG are implicated in disease. For example, the autism spectrum disorder Rett syndrome is caused by loss of a protein that reads methylated CG and affects the activity of genes. The Royal Society GlaxoSmithKline Prize Lecture is awarded for original contributions to medical and veterinary sciences published within ten years from the date of the award.]]> https://bioinformaticsonline.com/news/view/34369/scfbio-have-developed-sanjeevini Fri, 17 Nov 2017 07:55:49 -0600 https://bioinformaticsonline.com/news/view/34369/scfbio-have-developed-sanjeevini <![CDATA[SCFBio have developed Sanjeevini]]> SCFBio have developed a new android based application for drug design called Sanjeevini (https://play.google.com/store/apps/details?id=com.sanjeevini&hl=en). It is available free of charge. You can download it using Google play store. Just search for "Sanjeevini-SCFBIO-CADD" in Google play store. It contains all modules used by current Sanjeevini users. We have worked towards making a unified and easy to use interface. The app now supports all major small molecule file formats (pdb, mol, sdf, mol2 and xyz). The application contains inbuilt visualizer JSmol for easy analysis of results. Users can now directly download the protein files from PDB ("Get protein PDB file" in `FILE` Menu) and prepare it using the easy to use in-built module "Prepare protein/DNA".

SCFBio have worked towards making the process of Job retrieval more streamlined and user friendly. All jobs are now recorded in the "Job results". It can be accessed using the main page of the application. Job status can now be retrieved by clicking on the refresh button against the job ID.

SCFBio have also added a new feature of accessing Jobs run on different android application. Users can retrieve jobs run by other users by sharing the job ID and module name. This feature can be accessed using the Import Jobs option in File menu. We hope this feature will help collaborating groups stay in touch with each other.

The module contains all modules of Sanjeevini suite of software for structure based Drug design.

Sl No. Module name Activity
1 Prepare Protein/DNA Prepares protein/DNA for other modules of Sanjeevini
2 Prepare ligand Prepares ligands for other modules of Sanjeevini
3 Active site Prediction Predicts biologically relevant sites in a protein
4 ParDOCK Rigid Docking of Protein-Ligand complex
5 BAPPL Binding affinity prediction of Protein-Ligand complex
6 BAPPL Z Binding affinity prediction of Protein-Zinc-Ligand complex
7 DNA ligand Docking Rigid Docking of DNA-Ligand complex
8 PreDDICTA Binding affinity prediction of DNA-Ligand complex
9 SOM Prediction Rigid Docking of Ligand and CYP proteins
10 Lipinski filters Checks Lipinski's rule of five for ligand molecule
11 Molecular volume Calculates volume of a ligand
12 RASPD Virtual screening of protein molecule to yield hit molecules
13 AADS Prediction and docking of top 10 biologically relevant sites on protein
14 Intercalate Rigid Docking of DNA-Ligand complex in intercalation sites
15 DNA sequence to str. Converts DNA sequence to DNA structure (A-DNA or B-DNA)
16 NRDBSM Non-redundant database of small molecules
17 TPACM4 Partial charge calculator for small molecules
18 Wiener index Wiener index calculator for small molecules

The results can be downloaded to the PC desktop for further analysis. For this you can use this accompanying website for this purpose:
http://www.scfbio-iitd.res.in/sanjapp/webSearch/Sanjeevini_webpage.html

On more information on how to use the application please visit: http://scfbio-iitd.res.in/sanjapp/webSearch/doc.html
or
http://scfbio-iitd.res.in/sanjeeviniapp/tut.html

Please email us your valuable comments and suggestions at iitd.scfbio@gmail.com

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29583/graph-genome-suite Fri, 28 Oct 2016 07:59:54 -0500 https://bioinformaticsonline.com/bookmarks/view/29583/graph-genome-suite <![CDATA[Graph Genome Suite]]> Seven Bridges is the biomedical data analysis company accelerating breakthroughs in genomics research for cancer, drug development and precision medicine. We build self-improving systems to analyze millions of genomes, including the Graph Genome Suite — the most advanced population genomics tools in the world.

Address of the bookmark: https://www.sbgenomics.com/graph/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38745/osprey-network-visualization-system Sun, 20 Jan 2019 05:34:24 -0600 https://bioinformaticsonline.com/bookmarks/view/38745/osprey-network-visualization-system <![CDATA[Osprey: Network Visualization System]]> Osprey is a software platform for the visualization of complex biological interaction networks. Osprey builds data-rich graphical representations from Gene Ontology (GO) annotated interaction data maintained by the BioGRID.

Osprey is developed by the TyersLab and is a part of the BioGRID family of software. It utilizes both MySQL and Java to operate and is compatible with Windows, Linux, and Apple operating systems.

These works were published in Breitkreutz, BJ., Stark, C., Tyers M. "Osprey: A Network Visualization System." Genome Biology 2003 4(3):R22 [Genome Biology] [PDF] [PubMed] and supported by the National Institutes of Health, Canadian Institutes of Health Research, and Genome Canada.

Address of the bookmark: https://osprey.thebiogrid.org/

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/36111/d3networktools-for-creating-d3-javascript-network-tree-dendrogram-and-sankey-graphs-from-r Fri, 06 Apr 2018 12:10:45 -0500 https://bioinformaticsonline.com/bookmarks/view/36111/d3networktools-for-creating-d3-javascript-network-tree-dendrogram-and-sankey-graphs-from-r <![CDATA[d3Network:Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.]]> Mike Bostock’s D3.js is great for creating interactive network graphs with JavaScript. The d3Network package makes it easy to create these network graphs from R. The main idea is that you should able to take an R data frame with information about the relationships between members of a network and create full network graphs with one command.

Address of the bookmark: http://christophergandrud.github.io/d3Network/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40964/panev-an-r-package-for-a-pathway-based-network-visualization Sun, 09 Feb 2020 12:41:52 -0600 https://bioinformaticsonline.com/bookmarks/view/40964/panev-an-r-package-for-a-pathway-based-network-visualization <![CDATA[PANEV: an R package for a pathway-based network visualization]]> PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network visualization. Based on information available on KEGG, it visualizes genes within a network of multiple levels (from 1 to n) of interconnected upstream and downstream pathways. The network graph visualization helps to interpret functional profiles of a cluster of genes.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3371-7

Address of the bookmark: https://github.com/vpalombo/PANEV

]]> Jit https://bioinformaticsonline.com/bookmarks/view/26525/ensembl-comparative-genomics-resources Sun, 28 Feb 2016 17:10:20 -0600 https://bioinformaticsonline.com/bookmarks/view/26525/ensembl-comparative-genomics-resources <![CDATA[Ensembl comparative genomics resources]]>

The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.

Database URL: http://www.ensembl.org.

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/

]]> Jitendra Narayan https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources Tue, 28 Jun 2022 04:08:06 -0500 https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources <![CDATA[List of comparative genomics resources !]]>

Compare structural and functional annotations of proteins between sequenced genomes.

View AREs in the human transcriptome and study the comparative genomics of AREs in model organisms.

Find information about orthologous genes in prokaryotes.

Search for publicly available QTL data on livestocks and animal species.

Find information about bovine genomics data.

A multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species.

A database resource of developmentally associated conserved non-coding elements.

Delineate conserved non-coding blocks from upstream regions of putative orthologous gene pairs from man, mouse, rat, fugu, Mus musculus, Danio rerio, and zebrafish.

Find coexpressed gene lists and networks in human and mouse.

Construct phylogenetic tree of microorganisms based on oligopeptide content of their complete proteomes.

A novel database server that classifies GenBank's dbEST (database of expressed gene sequences) libraries and removes contaminants.

Find information about the ancestral relationship between genes.

Provides an overview of the genomic organization of microRNAs and extent of conservation during evolution in different metazoan species.

Conduct comparative biometric analysis of chromosomes of different organisms.

Search for Indices of gene and transcripts in human and mouse.

Search and compare 12 new and old Drosophila genomes.

Access to whole genome alignments of human, mouse, rat and fish sequences.

Find eukaryotic paralog/paralogon information.

Analyze the evolutionary process of overlapping genes when comparing different species.

The first publicly available system reported to handle inter-species gene mention normalization.

A web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes.

Visualize gene indices of human, mouse, Arabidopsis, Zebrafish, Drosophila and Sheep.

Find information about mutated mouse genes.

A data management and analysis system for metagenomes

Search for influenza sequence, vaccine, and drug resistance information.

LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal models for their research.

The missing link between multi-species full genome comparisons and functional analysis.

Conduct comparative analysis of completely sequenced microbial genomes.

A biologist-centric software for evolutionary analysis of DNA and protein sequences.

Conduct single nucleotide polymorphisms diversity measurements among homologous sequences from the Mammalia class.

Find information about 1000s of microbial genomes.

A database dedicated to the study of genome conservation.

Explore orthologous relations across 352 complete genomes.

Browse complete genomes in several clades.

A database of orthologous genomic markers for placental mammal phylogenetics.

Conduct genome wide functional and structural analysis.

Conduct genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes.

Compare phenotypes of a given gene or gene set in different model organisms.

Phylemon is a web server that integrates a selected suite of more than 20 different tools from the most popular stand-alone programs of phylogenetic and evolutionary analysis.

Use this database to see where in the evolution some phylogenetic lineages were started, and over which species they were contained.

Search for genomic information on nematode satellite species Pristionchus pacificus.

Find information about related protein sequences.

Database hosting genomics and post-genomics data from multiple protozoans.

A database of pseudogene families based on the protein families from the Pfam database.

Find genomic information about mammals.

Find information about predicted regulons in prokaryotic transcription regulation.

Perform systematic comparison of proteome data among species.

A comparative map viewer dedicated to the biology of the Solanaceae family.

Analyze data from functional analysis on fragmented microbial genetic material.

Visualize and explore comparative genomic hybridization data sets.

Search for genome-wide annotations of regulatory sites in yeast and prokaryotes genomes.

Search for information on adaptive evolution in gene families of higher plants and chordate.

Generate graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots.

Conduct a comprehensive analysis of genes and genomes.

An interactive online poster presentation on the Macaque genome, including high-quality images, video clips, and Web resources

Search for annotated genetic information of expressed sequence tags (ESTs) in different eukaryotic organisms.

Find mapping and expression information for a unigene cluster (ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene)

A public online resource for identifying or designing 'universal' overgo-hybridization probes from conserved sequences that can be used to efficiently screen one or more genomic libraries from a designated group of species.

Comprehensive suite of programs and databases for comparative analysis of genomic sequences.

Find metabolic networks and phylogenomic information on a taxonomically diverse range of eukaryotes.

]]> Shruti Paniwala https://bioinformaticsonline.com/pages/view/35559/computational-resources-for-te-discovery-and-te-detection Mon, 12 Feb 2018 10:29:18 -0600 https://bioinformaticsonline.com/pages/view/35559/computational-resources-for-te-discovery-and-te-detection <![CDATA[Computational resources for TE discovery and TE detection]]> Transposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis.

Following are the list of resource and location for TE discovery and TE detection:

BLASTER suite http://urgi.versailles.inra.fr/development/blaster/ 

Censor http://www.girinst.org/censor/download.php 

find_ltr http://darwin.informatics.indiana.edu/cgi-bin/evolution/ltr.pl 

FINDMITE http://jaketu.biochem.vt.edu/dl_software.htm

HMMER http://hmmer.janelia.org/

LTR_FINDER http://tlife.fudan.edu.cn/ltr_finder/

LTR_STRUC http://www.genetics.uga.edu/retrolab/data/LTR_Struc.html

LTR_MINER http://genomebiology.com/2004/5/10/R79/suppl/s7

LTR_par http://www.eecs.wsu.edu/~ananth/software.htm

MAK http://wesslercluster.plantbio.uga.edu/mak06.html

MaskerAid http://blast.wustl.edu/maskeraid/

mer-engine http://mer-engine.cshl.edu/mer-home.php

mreps http://bioinfo.lifl.fr/mreps/

PILER http://www.drive5.com/piler/

PLOTREP http://repeats.abc.hu/cgi-bin/plotrep.pl

RepBase http://www.girinst.org/

RepeatFinder http://cbcb.umd.edu/software/RepeatFinder/

RepeatGluer http://nbcr.sdsc.edu/euler/intro_tmp.htm

RepeatMasker http://www.repeatmasker.org/

RepeatRunner http://www.yandell-lab.org/repeat_runner/index.html

RepeatScout http://repeatscout.bioprojects.org/

repeat-match http://mummer.sourceforge.net/

REPuter http://www.genomes.de/

RetroMap http://www.burchsite.com/bioi/RetroMapHome.html

SMaRTFinder http://bioinf.dimi.uniud.it/software/software/smartfinder

Tandem Repeats Finder http://tandem.bu.edu/trf/trf.html

Transposon Cluster Finder http://www.mssm.edu/labs/warbup01/paper/files.html

TE nest http://www.plantgdb.org/prj/TE_nest/TE_nest.html

TRANSPO http://alggen.lsi.upc.es/recerca/search/transpo/transpo.html

TSDfinder http://www.ncbi.nlm.nih.gov/CBBresearch/Landsman/TSDfinder/

Tu Lab TE tools http://jaketu.biochem.vt.edu/dl_software.htm

WU-BLAST http://blast.wustl.edu

]]> Abhimanyu Singh https://bioinformaticsonline.com/blog/view/43898/online-resources-on-must-read-papers-in-evolutionary-biology-for-a-literature-club Tue, 28 Jun 2022 07:29:08 -0500 https://bioinformaticsonline.com/blog/view/43898/online-resources-on-must-read-papers-in-evolutionary-biology-for-a-literature-club <![CDATA[Online resources on must-read papers in evolutionary biology, for a literature club]]> 1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources for exploring the literature: Barton, N. H., Briggs, D. E. G., Eisen, J. A., Goldstein, D. B., & Patel, N. H. (2007). Evolution. Cold Spring Harbor Laboratory Press. - Papers from a course named "Classics in Evolutionary Biology": Evolutionary Synthesis 1. Haldane, J. B. S. 1932. The causes of evolution. Longmans. New York. (esp. Ch. IV). 2. Fisher, R. A. 1930. The genetical theory of natural selection. Oxford University Press, Oxford. Selected Sections - Fundamental Theorem. Genetic Variation 1a. Lewontin, R. C., and J. L. Hubby. 1966. A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics. 54:595-609. 1b. Sachidandam et al. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. 409: 928-33. 2. Wright S., Dobzhansky T., Hovanitz W. 1942 Genetics of natural populations VII The allelism of lethals in the third chromosome of Drosophila pseudoobscura. Genetics 27: 363-394. Recombination and evolution 1. Hill, W. G., and A. Robertson. 1966. The effect of linkage on limits to artificial selection. Genet. Res. 8:269-294. 2. Maynard Smith and Haigh. 1974. The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35. Understanding sequence variation 1. Begun D. J., Aquadro C. F., 1992 Levels of naturally occurring DNA polymorphism correlate with recombination rate in Drosophila melanogaster. Nature 356: 519-520. 2. Green R. E., Reich D., Pääbo S., 2010 A draft sequence of the Neandertal genome. Science 328: 710-722. Quantitative Genetics: variation in complex traits 1. Galton F., 1877 Typical laws of heredity. Nature 15: 492-495- 512-514- 532-533. 2. Turelli M., 1984 Heritable genetic variation via mutation-selection balance: Lerch's Zeta meets the abdominal bristle. Theor. Popul. Biol. 25: 138-193. Quantitative Genetics: finding the genes 1. Shrimpton A. E., Robertson A., 1988 The Isolation of polygenic factors controlling bristle score in Drosophila melanogaster II Distribution of third chromosome bristle effects within chromosome sections. Genetics 118: 445-459. 2. Boyle E. A., Li Y. I., Pritchard J. K., 2017 An expanded view of complex traits: from polygenic to omnigenic. Cell 169: 1177-1186. Neutral Evolution 1. Kimura, M. 1968. Evolutionary rate at the molecular level. Science. 217:624-626. 2a. Kern A. D., Hahn M. W., 2018 The Neutral Theory in Light of Natural Selection. Molecular Biology and Evolution 110: 21077-6. 2b. Jensen J. D., Payseur B. A., Stephan W., Aquadro C. F., Lynch M., Charlesworth D., Charlesworth B., 2018 The importance of the Neutral Theory in 1968 and 50 years on: a response to Kern and Hahn 2018. Evolution 112: 2109-4. 2c. Ellegren & Galtier. 2016. Determinants of genetic diversity. Nature Reviews Genetics. Mutation and Genetic Variability 1. Luria, S. E., and M. Delbrück. 1943. Mutations of Bacteria from Virus Sensitivity to Virus Resistance. Genetics. 28(6):491-511. 2. Hill, W G. 1982. "Rates of Change in Quantitative Traits From Fixation of New Mutations." Proceedings of the National Academy of Sciences (U.S.A.) 79: 142-45. Testing for selection 1. McDonald & Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 2. Begun, et al. Mol. Biol. Evol. 16, 1816-1819 (1999). 3. Siddiq et al. 2016. Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster. Nature Ecology & Evolution. The shifting balance 1. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proceedings of the VI International Congress of Genetics: 1. pp 356-366. 2. Coyne, J.A., N.H. Barton, and M. Turelli. 1997. A critique of Wright's shifting balance theory of evolution. Evolution 51: 643-671. 3. Barton. 2016. Sewall Wright on Evolution in Mendelian Populations and the "Shifting Balance". Genetics. Evolution of Sex 1. Muller, H.J. 1964. The relation of recombination to mutational advance. Mutation Res. 1(1):2-9 2. McDonald et al. 2016. Sex speeds adaptation by altering the dynamics of molecular evolution. Nature. Kin Selection, Cooperation, and Conflict 1. Hamilton, W. D. 1964. The genetical evolution of social behaviour I. Journal of Theoretical Biology. 7:1-52. 2. Trivers, R. L. 1974 Parent-offspring conflict. American Zoologist. 14(1):249-264. Sexual Selection 1. Zahavi, A. 1975. Mate selection - a selection of a handicap. J. Theor. Biol. 53:205-214. 2. Kirkpatrick, M., and Ryan, M.J. 1991. The evolution of mating preferences and the paradox of the lek. Nature. 350:33-38. Fitness Landscapes 1. Dean, A. 1995. A Molecular Investigation of Genotype by Environment Interactions. Genetics. 139:19-33. 2. Costanzo et al. 2010. The Genetic Landscape of a Cell. Science. Speciation 1. Coyne, J. A., and H. A. Orr. 1989. Patterns of speciation in Drosophila. Evolution. 43:362-381. 2. Corbett-Detig et al. 2013. Genetic incompatibilities are widespread within species. Nature. 2. *Marcos Antezana:* Valen, L. v. 1975. Energy and Evolution. University of Chicago, Department of Biology. 3. *Remco Folkertsma:* 1. The work by Hopi Hoekstra on local adaptation and oldfield mice 2. Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., Müller, I., ... & Wolf, J. B. (2014). The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science, 344(6190), 1410-1414. 4. *Joshka Kaufmann and Leslie Turner* They offer us a link to 'papers every evolutionary biologist should read', the papers are collected by Leslie Turner. https://static1.squarespace.com/static/53e8cb7ce4b02c4bc3aeeee4/t/5ab8fcb670a6ad55c67fcdf4/1522072758665/EvoBioClassicsRefList.pdf 5. *Sarah Stockwell* Matt Ridley collected classic papers in evolutionary biology and printed part of these papers in his book Evolution (see Matt Ridley. Evolution (Univ. of Oxford Press, 2nd edition, 2004))]]> Shruti Paniwala