<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/35559?offset=70 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/bookmarks/view/43943/bioinformatics-tutorial Mon, 22 Aug 2022 23:56:22 -0500 https://bioinformaticsonline.com/bookmarks/view/43943/bioinformatics-tutorial <![CDATA[Bioinformatics Tutorial !]]> This site aims to be a useful resource for bioinformatics beginners. Feel free to jump right in with the section most relevant to you, and if you're not sure, then the place to start is definitely Unix

Address of the bookmark: https://astrobiomike.github.io/

]]> Neel https://bioinformaticsonline.com/pages/view/35805/python-learning-resources-for-bioinformatics-and-computational-biologist Fri, 02 Mar 2018 06:54:15 -0600 https://bioinformaticsonline.com/pages/view/35805/python-learning-resources-for-bioinformatics-and-computational-biologist <![CDATA[Python learning resources for bioinformatics and computational biologist !]]> Python is a general-purpose language, which means it can be used to build just about anything, which will be made easy with the right tools/libraries.

Professionally, Python is great for backend web development, data analysis, artificial intelligence, and scientific computing. Many developers have also used Python to build productivity tools, games, and desktop apps, so there are plenty of resources to help you learn how to do those as well.

For pros and cons visit http://www.bestprogramminglanguagefor.me/why-learn-python and http://bioinformaticsonline.com/discussion/view/459/python-vs-perl

More resources at https://github.com/CodementorIO/Python-Learning-Resources

Following are the list of useful python programming resources:

]]> Jit https://bioinformaticsonline.com/blog/view/43900/finding-a-mimicry-game-for-teaching-on-line-and-mentioned-general-resources Tue, 28 Jun 2022 07:32:05 -0500 https://bioinformaticsonline.com/blog/view/43900/finding-a-mimicry-game-for-teaching-on-line-and-mentioned-general-resources <![CDATA[Finding a mimicry game for teaching on-line and mentioned general resources]]> Mimicry and other resources Mimicry games: Great Heliconius game: http://heliconius.org/evolving_butterflies/ (See also https://royalsocietypublishing.org/doi/10.1098/rspb.2020.0014) Other one, a bit less friendly: https://ccl.northwestern.edu/netlogo/models/Mimicry Camouflage practical https://alexis-catherine.github.io/publication/natural-selection-and-camouflage/ (NetLogo also has one: https://ccl.northwestern.edu/netlogo/models/BugHuntCamouflage) Peppered moth game: https://askabiologist.asu.edu/peppered-moths-game/play.html General resources The always popular Populus: https://cbs.umn.edu/populus/overview Drift & Gene Flow https://cartwrig.ht/apps/genie/ (Cock van Oosterhout has a great ppt to lead students through this) See also https://cartwrig.ht/apps/redlynx/ https://demonstrations.wolfram.com/ReplicatorMutatorDynamicsWithThreeStrategies/ NetLogo: http://ccl.northwestern.edu/netlogo/models/index.cgi Population Genetics: https://www.radford.edu/~rsheehy/Gen_flash/popgen/ Evolution in general https://evolution.berkeley.edu/evolibrary/home.php Mitochondrial Eve: https://projects.ncsu.edu/cals/gn/ex/mit-eve.html Y chromosomes: https://projects.ncsu.edu/cals/gn/ex/y-chrom.html A professional online package from Michael Kasumovic: https://arludo.com/ a compilation of resources: https://planted.botany.org/index.php?P=Home Finally, Donald Forsdyke has some great on-line videos explaining evolutionary principles (occasionally in a fake Scottish accent): http://post.queensu.ca/~forsdyke/videolectures.htm

 

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/34501/dnapipete-de-novo-assembly-annotation-pipeline-for-transposable-elements Sat, 02 Dec 2017 18:25:44 -0600 https://bioinformaticsonline.com/bookmarks/view/34501/dnapipete-de-novo-assembly-annotation-pipeline-for-transposable-elements <![CDATA[dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements]]> dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

Frontoutput examples of quantification and TE landscape (relative age) produced by dnaPipeTE

 

Address of the bookmark: https://github.com/clemgoub/dnaPipeTE

]]> Rahul Nayak https://bioinformaticsonline.com/researchlabs/view/43293/josefa-gonzalez-lab Thu, 19 Aug 2021 08:52:56 -0500 <![CDATA[Josefa González Lab]]> Lab focus on understanding how organisms adapt to their environments. They combine omics approaches with detailed molecular and phenotypic analyses to get a comprehensive picture of adaptation. Our aim at being internationally recognized as a leading lab in the field of environmental adaptation.
Lab share our passion for science with the general public by leading outreach projects aimed at increasing science awareness.

More at https://www.biologiaevolutiva.org/gonzalez_lab/

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